Starting phenix.real_space_refine on Thu Jan 18 15:15:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0p_34413/01_2024/8h0p_34413.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0p_34413/01_2024/8h0p_34413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0p_34413/01_2024/8h0p_34413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0p_34413/01_2024/8h0p_34413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0p_34413/01_2024/8h0p_34413.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0p_34413/01_2024/8h0p_34413.pdb" } resolution = 3.15 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5682 2.51 5 N 1531 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 103": "NH1" <-> "NH2" Residue "R TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 261": "NH1" <-> "NH2" Residue "R ARG 263": "NH1" <-> "NH2" Residue "R PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8932 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 2 Chain: "R" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2305 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 3 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1768 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "E" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Time building chain proxies: 5.18, per 1000 atoms: 0.58 Number of scatterers: 8932 At special positions: 0 Unit cell: (124.8, 92.56, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1657 8.00 N 1531 7.00 C 5682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.4% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'L' and resid 22 through 26 removed outlier: 3.619A pdb=" N ALA L 25 " --> pdb=" O ASN L 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 70 Proline residue: R 47 - end of helix Processing helix chain 'R' and resid 79 through 106 removed outlier: 3.932A pdb=" N VAL R 97 " --> pdb=" O LEU R 93 " (cutoff:3.500A) Proline residue: R 98 - end of helix Processing helix chain 'R' and resid 112 through 147 Proline residue: R 120 - end of helix Processing helix chain 'R' and resid 156 through 174 Processing helix chain 'R' and resid 176 through 181 removed outlier: 4.064A pdb=" N VAL R 180 " --> pdb=" O VAL R 176 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE R 181 " --> pdb=" O PRO R 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 176 through 181' Processing helix chain 'R' and resid 206 through 221 removed outlier: 3.954A pdb=" N LYS R 210 " --> pdb=" O GLU R 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL R 214 " --> pdb=" O LYS R 210 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL R 219 " --> pdb=" O LEU R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 244 removed outlier: 3.544A pdb=" N ILE R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 292 removed outlier: 3.541A pdb=" N THR R 260 " --> pdb=" O LYS R 256 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU R 269 " --> pdb=" O ALA R 265 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 3.619A pdb=" N PHE R 291 " --> pdb=" O MET R 287 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN R 292 " --> pdb=" O TYR R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 314 removed outlier: 3.747A pdb=" N LEU R 312 " --> pdb=" O VAL R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 328 removed outlier: 3.689A pdb=" N ASN R 320 " --> pdb=" O ASN R 316 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 329 through 342 removed outlier: 3.773A pdb=" N HIS R 334 " --> pdb=" O SER R 330 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU R 339 " --> pdb=" O PHE R 335 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N CYS R 340 " --> pdb=" O ASN R 336 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS R 341 " --> pdb=" O SER R 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.541A pdb=" N VAL A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 215 through 221 removed outlier: 3.562A pdb=" N CYS A 219 " --> pdb=" O TRP A 216 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 221 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.654A pdb=" N ALA A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 removed outlier: 3.597A pdb=" N VAL A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.525A pdb=" N PHE A 295 " --> pdb=" O PHE A 292 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 296 " --> pdb=" O PRO A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 296' Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.762A pdb=" N ILE A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.813A pdb=" N ILE A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'E' and resid 27 through 31 removed outlier: 3.546A pdb=" N PHE E 31 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.742A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 28 through 44 removed outlier: 3.746A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 183 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 195 removed outlier: 3.684A pdb=" N ALA A 225 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 56 removed outlier: 4.419A pdb=" N ARG B 51 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.701A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 93 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.926A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.884A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 207 removed outlier: 4.108A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.781A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.004A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.396A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.396A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 186 through 187 423 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2892 1.34 - 1.46: 2132 1.46 - 1.58: 3998 1.58 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 9113 Sorted by residual: bond pdb=" C TYR E 235 " pdb=" N PRO E 236 " ideal model delta sigma weight residual 1.334 1.359 -0.026 2.34e-02 1.83e+03 1.19e+00 bond pdb=" CB PRO R 298 " pdb=" CG PRO R 298 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.12e-01 bond pdb=" CA ILE R 46 " pdb=" CB ILE R 46 " ideal model delta sigma weight residual 1.537 1.540 -0.004 5.00e-03 4.00e+04 4.92e-01 bond pdb=" CA THR B 201 " pdb=" CB THR B 201 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 4.77e-01 bond pdb=" C ILE R 223 " pdb=" N PRO R 224 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.00e-01 ... (remaining 9108 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 262 107.34 - 114.00: 5147 114.00 - 120.66: 3692 120.66 - 127.32: 3148 127.32 - 133.97: 90 Bond angle restraints: 12339 Sorted by residual: angle pdb=" C VAL R 45 " pdb=" N ILE R 46 " pdb=" CA ILE R 46 " ideal model delta sigma weight residual 120.43 122.95 -2.52 9.60e-01 1.09e+00 6.92e+00 angle pdb=" C ILE R 46 " pdb=" CA ILE R 46 " pdb=" CB ILE R 46 " ideal model delta sigma weight residual 113.70 111.21 2.49 9.50e-01 1.11e+00 6.87e+00 angle pdb=" C ASP B 200 " pdb=" N THR B 201 " pdb=" CA THR B 201 " ideal model delta sigma weight residual 121.54 126.32 -4.78 1.91e+00 2.74e-01 6.26e+00 angle pdb=" C HIS L 28 " pdb=" N PHE L 29 " pdb=" CA PHE L 29 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.43e+00 angle pdb=" C TRP R 279 " pdb=" N PHE R 280 " pdb=" CA PHE R 280 " ideal model delta sigma weight residual 120.09 122.37 -2.28 1.25e+00 6.40e-01 3.32e+00 ... (remaining 12334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 5243 15.92 - 31.85: 146 31.85 - 47.77: 25 47.77 - 63.69: 5 63.69 - 79.61: 1 Dihedral angle restraints: 5420 sinusoidal: 2120 harmonic: 3300 Sorted by residual: dihedral pdb=" N PHE B 239 " pdb=" CA PHE B 239 " pdb=" CB PHE B 239 " pdb=" CG PHE B 239 " ideal model delta sinusoidal sigma weight residual -180.00 -126.84 -53.16 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" N TYR B 64 " pdb=" CA TYR B 64 " pdb=" CB TYR B 64 " pdb=" CG TYR B 64 " ideal model delta sinusoidal sigma weight residual -60.00 -109.61 49.61 3 1.50e+01 4.44e-03 8.80e+00 dihedral pdb=" CA ARG A 214 " pdb=" CB ARG A 214 " pdb=" CG ARG A 214 " pdb=" CD ARG A 214 " ideal model delta sinusoidal sigma weight residual -60.00 -107.57 47.57 3 1.50e+01 4.44e-03 8.51e+00 ... (remaining 5417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 860 0.026 - 0.052: 338 0.052 - 0.078: 118 0.078 - 0.104: 61 0.104 - 0.130: 28 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE B 128 " pdb=" N ILE B 128 " pdb=" C ILE B 128 " pdb=" CB ILE B 128 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE B 237 " pdb=" N ILE B 237 " pdb=" C ILE B 237 " pdb=" CB ILE B 237 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1402 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 73 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO E 74 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS R 208 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO R 209 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO R 209 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 209 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 280 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO R 281 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO R 281 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 281 " 0.015 5.00e-02 4.00e+02 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 809 2.75 - 3.28: 8844 3.28 - 3.82: 15069 3.82 - 4.36: 17608 4.36 - 4.90: 30529 Nonbonded interactions: 72859 Sorted by model distance: nonbonded pdb=" OD1 ASP B 168 " pdb=" OG1 THR B 170 " model vdw 2.208 2.440 nonbonded pdb=" OG SER B 250 " pdb=" OD1 ASP B 252 " model vdw 2.214 2.440 nonbonded pdb=" OG SER E 204 " pdb=" OG1 THR E 215 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR B 70 " pdb=" O PRO B 112 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR R 201 " pdb=" OH TYR R 286 " model vdw 2.279 2.440 ... (remaining 72854 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 2.240 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.570 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 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 : 0.001 0.039 9113 Z= 0.100 Angle : 0.405 5.736 12339 Z= 0.239 Chirality : 0.037 0.130 1405 Planarity : 0.003 0.030 1560 Dihedral : 7.539 79.614 3281 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.33 % 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: -2.49 (0.22), residues: 1108 helix: -0.63 (0.24), residues: 393 sheet: -1.49 (0.29), residues: 273 loop : -2.63 (0.24), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 87 HIS 0.002 0.000 HIS L 28 PHE 0.008 0.001 PHE B 258 TYR 0.006 0.001 TYR E 235 ARG 0.001 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 1.021 Fit side-chains REVERT: R 107 ASP cc_start: 0.6990 (t70) cc_final: 0.6711 (t70) REVERT: R 165 MET cc_start: 0.3785 (mmt) cc_final: 0.3467 (mtt) REVERT: A 256 LYS cc_start: 0.8066 (tttt) cc_final: 0.7795 (tttp) REVERT: B 222 MET cc_start: 0.4748 (mmm) cc_final: 0.4535 (ppp) REVERT: E 29 SER cc_start: 0.7431 (t) cc_final: 0.6915 (m) outliers start: 1 outliers final: 1 residues processed: 216 average time/residue: 0.2848 time to fit residues: 80.5274 Evaluate side-chains 151 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0770 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.0970 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 123 GLN R 212 HIS R 257 GLN ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 320 ASN ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 195 GLN A 209 GLN B 21 ASN B 264 GLN E 34 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 HIS E 183 GLN E 194 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9113 Z= 0.225 Angle : 0.544 6.842 12339 Z= 0.278 Chirality : 0.043 0.203 1405 Planarity : 0.004 0.035 1560 Dihedral : 3.686 55.340 1230 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.73 % Allowed : 7.94 % Favored : 90.33 % 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: -1.12 (0.25), residues: 1108 helix: 0.63 (0.26), residues: 392 sheet: -1.10 (0.30), residues: 272 loop : -1.69 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 24 HIS 0.010 0.002 HIS B 96 PHE 0.015 0.002 PHE E 67 TYR 0.013 0.002 TYR A 36 ARG 0.005 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: R 107 ASP cc_start: 0.7183 (t70) cc_final: 0.6878 (t70) REVERT: R 165 MET cc_start: 0.4405 (mmt) cc_final: 0.4006 (mtt) REVERT: A 294 GLU cc_start: 0.6743 (mp0) cc_final: 0.6398 (mm-30) REVERT: E 220 GLU cc_start: 0.6688 (mp0) cc_final: 0.6290 (mp0) outliers start: 17 outliers final: 10 residues processed: 182 average time/residue: 0.2463 time to fit residues: 59.1851 Evaluate side-chains 148 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 40 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 ASN R 283 HIS A 342 ASN B 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 9113 Z= 0.381 Angle : 0.665 8.708 12339 Z= 0.346 Chirality : 0.046 0.148 1405 Planarity : 0.005 0.045 1560 Dihedral : 4.863 58.212 1230 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.16 % Allowed : 9.27 % Favored : 87.58 % 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: -1.01 (0.25), residues: 1108 helix: 0.43 (0.26), residues: 401 sheet: -1.06 (0.29), residues: 281 loop : -1.34 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 68 HIS 0.008 0.003 HIS B 96 PHE 0.022 0.003 PHE B 185 TYR 0.024 0.003 TYR E 190 ARG 0.006 0.001 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 0.947 Fit side-chains REVERT: R 110 MET cc_start: 0.7002 (mmm) cc_final: 0.6795 (mmm) REVERT: R 151 MET cc_start: 0.4637 (tpt) cc_final: 0.3975 (mtt) REVERT: R 219 VAL cc_start: 0.8345 (p) cc_final: 0.8138 (t) REVERT: B 51 ARG cc_start: 0.6630 (ttp80) cc_final: 0.6328 (ttp80) REVERT: B 129 TYR cc_start: 0.8593 (m-80) cc_final: 0.8295 (m-80) REVERT: E 99 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8054 (mt) outliers start: 31 outliers final: 17 residues processed: 178 average time/residue: 0.2375 time to fit residues: 56.6637 Evaluate side-chains 149 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASN Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 0.0770 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 ASN R 292 ASN A 49 ASN A 202 HIS A 218 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN B 49 GLN B 235 ASN B 264 GLN E 194 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9113 Z= 0.181 Angle : 0.511 7.007 12339 Z= 0.263 Chirality : 0.041 0.137 1405 Planarity : 0.004 0.039 1560 Dihedral : 4.319 58.775 1230 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.83 % Allowed : 12.32 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1108 helix: 0.88 (0.27), residues: 391 sheet: -0.92 (0.30), residues: 275 loop : -1.14 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.006 0.001 HIS B 147 PHE 0.015 0.001 PHE A 194 TYR 0.011 0.001 TYR B 269 ARG 0.009 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.088 Fit side-chains REVERT: R 151 MET cc_start: 0.4879 (tpt) cc_final: 0.4243 (mtt) REVERT: R 165 MET cc_start: 0.5616 (mmp) cc_final: 0.5347 (mmp) REVERT: R 219 VAL cc_start: 0.8354 (p) cc_final: 0.8099 (t) REVERT: A 202 HIS cc_start: 0.7816 (m-70) cc_final: 0.7534 (m-70) REVERT: B 51 ARG cc_start: 0.6598 (ttp80) cc_final: 0.6250 (ttp80) REVERT: B 202 ARG cc_start: 0.7635 (mmt-90) cc_final: 0.7376 (mmt-90) REVERT: E 99 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8012 (mt) outliers start: 18 outliers final: 14 residues processed: 155 average time/residue: 0.2568 time to fit residues: 53.4442 Evaluate side-chains 151 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.0270 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 ASN R 316 ASN A 49 ASN A 202 HIS A 218 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN B 49 GLN B 235 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9113 Z= 0.191 Angle : 0.499 6.572 12339 Z= 0.256 Chirality : 0.041 0.139 1405 Planarity : 0.004 0.038 1560 Dihedral : 4.253 59.473 1230 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.34 % Allowed : 12.63 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.26), residues: 1108 helix: 1.10 (0.27), residues: 388 sheet: -0.95 (0.30), residues: 280 loop : -0.92 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 24 HIS 0.005 0.001 HIS A 327 PHE 0.013 0.001 PHE A 194 TYR 0.011 0.001 TYR B 269 ARG 0.010 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.039 Fit side-chains REVERT: R 106 PHE cc_start: 0.6347 (m-80) cc_final: 0.6030 (m-80) REVERT: R 151 MET cc_start: 0.4931 (tpt) cc_final: 0.4324 (mtt) REVERT: R 165 MET cc_start: 0.5646 (mmp) cc_final: 0.5399 (mmp) REVERT: R 219 VAL cc_start: 0.8374 (p) cc_final: 0.8137 (t) REVERT: B 51 ARG cc_start: 0.6600 (ttp80) cc_final: 0.6269 (ttp80) REVERT: B 222 MET cc_start: 0.7199 (mmm) cc_final: 0.6967 (mmm) REVERT: E 99 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8083 (mt) outliers start: 23 outliers final: 17 residues processed: 155 average time/residue: 0.2523 time to fit residues: 51.8910 Evaluate side-chains 152 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.0060 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 ASN A 49 ASN A 218 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9113 Z= 0.311 Angle : 0.569 7.146 12339 Z= 0.294 Chirality : 0.043 0.154 1405 Planarity : 0.004 0.042 1560 Dihedral : 4.541 59.761 1230 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.44 % Allowed : 13.65 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1108 helix: 0.85 (0.27), residues: 394 sheet: -0.80 (0.30), residues: 263 loop : -0.99 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 104 HIS 0.007 0.002 HIS A 322 PHE 0.014 0.002 PHE A 194 TYR 0.013 0.002 TYR B 269 ARG 0.012 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 1.049 Fit side-chains REVERT: R 106 PHE cc_start: 0.6399 (m-80) cc_final: 0.6067 (m-80) REVERT: R 151 MET cc_start: 0.4971 (tpt) cc_final: 0.4300 (mtt) REVERT: R 219 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8172 (t) REVERT: B 51 ARG cc_start: 0.6569 (ttp80) cc_final: 0.6254 (ttp80) REVERT: E 99 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8124 (mt) outliers start: 24 outliers final: 20 residues processed: 138 average time/residue: 0.2606 time to fit residues: 47.5918 Evaluate side-chains 138 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 ASN A 218 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9113 Z= 0.184 Angle : 0.506 6.978 12339 Z= 0.260 Chirality : 0.041 0.157 1405 Planarity : 0.004 0.053 1560 Dihedral : 4.343 59.795 1230 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.44 % Allowed : 14.26 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1108 helix: 1.05 (0.27), residues: 388 sheet: -0.77 (0.31), residues: 265 loop : -0.90 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.005 0.001 HIS A 327 PHE 0.014 0.001 PHE A 194 TYR 0.011 0.001 TYR B 269 ARG 0.013 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 0.956 Fit side-chains REVERT: R 106 PHE cc_start: 0.6491 (m-80) cc_final: 0.6184 (m-80) REVERT: R 151 MET cc_start: 0.5075 (tpt) cc_final: 0.4406 (mtt) REVERT: R 219 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8130 (t) REVERT: B 24 ARG cc_start: 0.6277 (ttp-110) cc_final: 0.5297 (ptm-80) REVERT: B 51 ARG cc_start: 0.6520 (ttp80) cc_final: 0.6201 (ttp80) REVERT: B 222 MET cc_start: 0.7239 (mmm) cc_final: 0.6996 (mmm) REVERT: E 99 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8185 (mt) REVERT: E 192 MET cc_start: 0.5770 (mtp) cc_final: 0.5497 (mtp) outliers start: 24 outliers final: 17 residues processed: 136 average time/residue: 0.2696 time to fit residues: 48.2825 Evaluate side-chains 141 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 ASN A 218 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 235 ASN G 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9113 Z= 0.237 Angle : 0.527 7.151 12339 Z= 0.270 Chirality : 0.042 0.165 1405 Planarity : 0.004 0.050 1560 Dihedral : 4.411 59.752 1230 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.55 % Allowed : 14.56 % Favored : 82.89 % 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: -0.32 (0.26), residues: 1108 helix: 1.03 (0.27), residues: 389 sheet: -0.73 (0.31), residues: 265 loop : -0.89 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 263 HIS 0.006 0.001 HIS A 327 PHE 0.014 0.002 PHE A 194 TYR 0.012 0.001 TYR B 269 ARG 0.013 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.026 Fit side-chains REVERT: R 106 PHE cc_start: 0.6522 (m-80) cc_final: 0.6165 (m-80) REVERT: R 151 MET cc_start: 0.5167 (tpt) cc_final: 0.4552 (mtt) REVERT: R 219 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8271 (t) REVERT: B 51 ARG cc_start: 0.6538 (ttp80) cc_final: 0.6221 (ttp80) REVERT: B 222 MET cc_start: 0.7252 (mmm) cc_final: 0.7023 (mmm) REVERT: B 308 ASP cc_start: 0.7741 (p0) cc_final: 0.7520 (p0) REVERT: E 99 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8146 (mt) REVERT: E 192 MET cc_start: 0.5877 (mtp) cc_final: 0.5638 (mtp) outliers start: 25 outliers final: 20 residues processed: 137 average time/residue: 0.2775 time to fit residues: 50.0415 Evaluate side-chains 141 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 ASN A 218 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9113 Z= 0.205 Angle : 0.516 7.672 12339 Z= 0.263 Chirality : 0.041 0.166 1405 Planarity : 0.004 0.054 1560 Dihedral : 4.362 59.623 1230 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.44 % Allowed : 14.87 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1108 helix: 1.07 (0.27), residues: 389 sheet: -0.73 (0.31), residues: 265 loop : -0.85 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 263 HIS 0.005 0.001 HIS A 327 PHE 0.014 0.001 PHE A 194 TYR 0.011 0.001 TYR B 269 ARG 0.013 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.030 Fit side-chains REVERT: R 106 PHE cc_start: 0.6511 (m-80) cc_final: 0.6173 (m-80) REVERT: R 151 MET cc_start: 0.5198 (tpt) cc_final: 0.4565 (mtt) REVERT: R 219 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8261 (t) REVERT: B 51 ARG cc_start: 0.6533 (ttp80) cc_final: 0.6213 (ttp80) REVERT: B 308 ASP cc_start: 0.7600 (p0) cc_final: 0.7357 (p0) REVERT: E 99 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8184 (mt) outliers start: 24 outliers final: 21 residues processed: 135 average time/residue: 0.2581 time to fit residues: 46.1768 Evaluate side-chains 138 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.7039 > 50: distance: 69 - 88: 27.777 distance: 80 - 88: 26.570 distance: 88 - 89: 34.774 distance: 89 - 90: 9.476 distance: 89 - 92: 17.431 distance: 90 - 91: 34.898 distance: 90 - 93: 15.780 distance: 93 - 94: 18.207 distance: 94 - 95: 31.590 distance: 94 - 97: 36.188 distance: 95 - 96: 19.576 distance: 95 - 102: 32.831 distance: 97 - 98: 22.821 distance: 98 - 99: 16.099 distance: 99 - 100: 15.633 distance: 100 - 101: 11.371 distance: 102 - 103: 10.051 distance: 103 - 104: 25.096 distance: 103 - 106: 7.420 distance: 104 - 105: 25.379 distance: 104 - 111: 16.760 distance: 106 - 107: 33.294 distance: 107 - 108: 15.789 distance: 108 - 109: 20.631 distance: 108 - 110: 34.363 distance: 111 - 112: 24.781 distance: 112 - 113: 31.285 distance: 112 - 115: 18.715 distance: 113 - 114: 29.999 distance: 113 - 119: 36.110 distance: 115 - 116: 15.324 distance: 116 - 117: 29.782 distance: 116 - 118: 24.166 distance: 119 - 120: 21.755 distance: 119 - 125: 35.712 distance: 120 - 121: 22.129 distance: 120 - 123: 18.735 distance: 121 - 122: 31.871 distance: 121 - 126: 32.947 distance: 123 - 124: 12.395 distance: 124 - 125: 25.570 distance: 126 - 127: 32.948 distance: 127 - 128: 30.653 distance: 127 - 130: 29.809 distance: 128 - 129: 18.084 distance: 128 - 134: 15.745 distance: 130 - 131: 42.909 distance: 131 - 132: 36.630 distance: 131 - 133: 50.309 distance: 134 - 135: 13.056 distance: 135 - 136: 13.005 distance: 135 - 138: 47.556 distance: 136 - 137: 44.943 distance: 136 - 142: 27.312 distance: 138 - 139: 24.732 distance: 139 - 140: 33.622 distance: 139 - 141: 36.238 distance: 142 - 143: 54.681 distance: 143 - 144: 57.024 distance: 143 - 146: 30.591 distance: 144 - 145: 40.333 distance: 144 - 149: 24.474 distance: 146 - 147: 22.262 distance: 146 - 148: 22.412 distance: 149 - 150: 27.981 distance: 149 - 155: 26.847 distance: 150 - 151: 58.179 distance: 150 - 153: 38.323 distance: 151 - 152: 12.290 distance: 151 - 156: 47.497 distance: 153 - 154: 27.853 distance: 154 - 155: 55.138 distance: 156 - 157: 38.926 distance: 157 - 158: 57.760 distance: 157 - 160: 4.169 distance: 158 - 159: 44.618 distance: 158 - 163: 29.775 distance: 160 - 161: 40.674 distance: 160 - 162: 43.176