Starting phenix.real_space_refine on Fri Oct 11 00:44:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/10_2024/8j22_35942_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/10_2024/8j22_35942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/10_2024/8j22_35942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/10_2024/8j22_35942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/10_2024/8j22_35942_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/10_2024/8j22_35942_neut.cif" } resolution = 3.2 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= 0.001 sd= 0.022 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 S 58 5.16 5 Cl 1 4.86 5 C 5654 2.51 5 N 1505 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 8856 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "B" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1693 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2285 Classifications: {'peptide': 285} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 269} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "F" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1805 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'9UJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.32, per 1000 atoms: 0.60 Number of scatterers: 8856 At special positions: 0 Unit cell: (116.48, 111.28, 123.76, 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) Cl 1 17.00 S 58 16.00 O 1638 8.00 N 1505 7.00 C 5654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 82 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 38.1% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.575A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.761A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 51' Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.504A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.577A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.591A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.915A pdb=" N ALA B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 removed outlier: 3.546A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 38 removed outlier: 3.820A pdb=" N MET C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) Proline residue: C 23 - end of helix removed outlier: 3.585A pdb=" N LEU C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 61 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.524A pdb=" N LYS C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 113 removed outlier: 3.856A pdb=" N CYS C 82 " --> pdb=" O PRO C 78 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 122 through 152 removed outlier: 4.002A pdb=" N GLY C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 188 removed outlier: 3.655A pdb=" N LEU C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 188 through 208 removed outlier: 3.880A pdb=" N THR C 208 " --> pdb=" O TRP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 235 removed outlier: 4.050A pdb=" N LEU C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 249 removed outlier: 4.005A pdb=" N ASN C 239 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS C 242 " --> pdb=" O TYR C 238 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 273 removed outlier: 3.685A pdb=" N ASN C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 276 through 291 removed outlier: 4.058A pdb=" N VAL C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 20 Processing helix chain 'D' and resid 25 through 40 Processing helix chain 'D' and resid 41 through 44 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.650A pdb=" N ASP F 90 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'F' and resid 206 through 210 removed outlier: 3.942A pdb=" N VAL F 210 " --> pdb=" O ALA F 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 49 removed outlier: 5.312A pdb=" N THR A 45 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN A 338 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 47 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 61 removed outlier: 3.717A pdb=" N ALA A 58 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 72 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP A 81 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS A 87 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 103 removed outlier: 7.011A pdb=" N GLY A 113 " --> pdb=" O MET A 99 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS A 101 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA A 111 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TYR A 103 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR A 109 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS A 119 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU A 136 " --> pdb=" O CYS A 119 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 121 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 132 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 149 removed outlier: 3.500A pdb=" N ILE A 155 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 159 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP A 168 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 174 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.977A pdb=" N SER A 187 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 200 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 218 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP A 210 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS A 216 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 232 removed outlier: 4.010A pdb=" N SER A 243 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS A 248 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR A 261 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A 250 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 252 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 257 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 274 through 276 removed outlier: 3.739A pdb=" N GLY A 304 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP A 296 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG A 302 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 191 removed outlier: 9.097A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.503A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 126 through 128 removed outlier: 3.647A pdb=" N VAL F 141 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 197 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 133 through 135 removed outlier: 3.758A pdb=" N GLY F 211 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP F 162 " --> pdb=" O LEU F 174 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1215 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: 2.56 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2852 1.35 - 1.47: 2285 1.47 - 1.60: 3826 1.60 - 1.72: 3 1.72 - 1.84: 83 Bond restraints: 9049 Sorted by residual: bond pdb=" C13 9UJ C 401 " pdb=" C15 9UJ C 401 " ideal model delta sigma weight residual 1.502 1.588 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C09 9UJ C 401 " pdb=" N07 9UJ C 401 " ideal model delta sigma weight residual 1.483 1.564 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" N08 9UJ C 401 " pdb=" O06 9UJ C 401 " ideal model delta sigma weight residual 1.406 1.334 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C13 9UJ C 401 " pdb=" N07 9UJ C 401 " ideal model delta sigma weight residual 1.366 1.427 -0.061 2.00e-02 2.50e+03 9.38e+00 bond pdb=" C16 9UJ C 401 " pdb="CL01 9UJ C 401 " ideal model delta sigma weight residual 1.756 1.702 0.054 2.00e-02 2.50e+03 7.17e+00 ... (remaining 9044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.45: 12252 5.45 - 10.89: 17 10.89 - 16.34: 3 16.34 - 21.79: 1 21.79 - 27.24: 1 Bond angle restraints: 12274 Sorted by residual: angle pdb=" C PHE C 73 " pdb=" N ARG C 74 " pdb=" CA ARG C 74 " ideal model delta sigma weight residual 121.70 148.94 -27.24 1.80e+00 3.09e-01 2.29e+02 angle pdb=" C TYR F 221 " pdb=" N PRO F 222 " pdb=" CA PRO F 222 " ideal model delta sigma weight residual 119.84 131.77 -11.93 1.25e+00 6.40e-01 9.11e+01 angle pdb=" N TYR F 221 " pdb=" CA TYR F 221 " pdb=" C TYR F 221 " ideal model delta sigma weight residual 109.81 129.39 -19.58 2.21e+00 2.05e-01 7.85e+01 angle pdb=" C PRO F 222 " pdb=" CA PRO F 222 " pdb=" CB PRO F 222 " ideal model delta sigma weight residual 111.56 125.73 -14.17 1.65e+00 3.67e-01 7.38e+01 angle pdb=" CA PRO A 234 " pdb=" N PRO A 234 " pdb=" CD PRO A 234 " ideal model delta sigma weight residual 112.00 103.43 8.57 1.40e+00 5.10e-01 3.75e+01 ... (remaining 12269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 4809 23.85 - 47.69: 479 47.69 - 71.54: 62 71.54 - 95.39: 6 95.39 - 119.23: 1 Dihedral angle restraints: 5357 sinusoidal: 2081 harmonic: 3276 Sorted by residual: dihedral pdb=" CA TYR F 221 " pdb=" C TYR F 221 " pdb=" N PRO F 222 " pdb=" CA PRO F 222 " ideal model delta harmonic sigma weight residual 180.00 60.77 119.23 0 5.00e+00 4.00e-02 5.69e+02 dihedral pdb=" C TYR F 221 " pdb=" N TYR F 221 " pdb=" CA TYR F 221 " pdb=" CB TYR F 221 " ideal model delta harmonic sigma weight residual -122.60 -149.63 27.03 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" N TYR F 221 " pdb=" C TYR F 221 " pdb=" CA TYR F 221 " pdb=" CB TYR F 221 " ideal model delta harmonic sigma weight residual 122.80 149.59 -26.79 0 2.50e+00 1.60e-01 1.15e+02 ... (remaining 5354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 1387 0.250 - 0.500: 1 0.500 - 0.750: 0 0.750 - 1.000: 2 1.000 - 1.250: 1 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA TYR F 221 " pdb=" N TYR F 221 " pdb=" C TYR F 221 " pdb=" CB TYR F 221 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.91e+01 chirality pdb=" CA PHE C 73 " pdb=" N PHE C 73 " pdb=" C PHE C 73 " pdb=" CB PHE C 73 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA PRO F 222 " pdb=" N PRO F 222 " pdb=" C PRO F 222 " pdb=" CB PRO F 222 " both_signs ideal model delta sigma weight residual False 2.72 1.91 0.81 2.00e-01 2.50e+01 1.65e+01 ... (remaining 1388 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 233 " -0.084 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO A 234 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 221 " -0.064 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO F 222 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO F 222 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO F 222 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 275 " -0.014 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C PHE C 275 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE C 275 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 276 " -0.015 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 85 2.60 - 3.18: 6964 3.18 - 3.75: 13761 3.75 - 4.33: 18753 4.33 - 4.90: 31780 Nonbonded interactions: 71343 Sorted by model distance: nonbonded pdb=" OE2 GLU A 258 " pdb=" OG1 THR A 261 " model vdw 2.029 3.040 nonbonded pdb=" O ILE C 16 " pdb=" OG1 THR C 20 " model vdw 2.166 3.040 nonbonded pdb=" O SER A 96 " pdb=" OG SER A 96 " model vdw 2.226 3.040 nonbonded pdb=" O GLN C 148 " pdb=" OG1 THR C 152 " model vdw 2.257 3.040 nonbonded pdb=" O GLN A 73 " pdb=" OG SER A 96 " model vdw 2.271 3.040 ... (remaining 71338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.04 max=1.00 mean=0.99 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.003 0.113 9049 Z= 0.225 Angle : 0.644 27.235 12274 Z= 0.329 Chirality : 0.061 1.250 1391 Planarity : 0.005 0.122 1552 Dihedral : 17.811 119.232 3241 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.42 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 31.07 % Favored : 68.93 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.86 % Twisted General : 0.09 % 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: 1.17 (0.26), residues: 1116 helix: 1.69 (0.26), residues: 397 sheet: 1.36 (0.32), residues: 298 loop : -0.52 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 75 HIS 0.002 0.000 HIS F 35 PHE 0.020 0.001 PHE C 197 TYR 0.007 0.001 TYR F 221 ARG 0.007 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6877 (m-30) cc_final: 0.6655 (m-30) REVERT: C 120 SER cc_start: 0.7960 (m) cc_final: 0.7505 (p) REVERT: F 183 SER cc_start: 0.8246 (m) cc_final: 0.7935 (p) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2507 time to fit residues: 55.1273 Evaluate side-chains 153 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 213 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 9049 Z= 0.254 Angle : 0.620 16.569 12274 Z= 0.326 Chirality : 0.044 0.305 1391 Planarity : 0.004 0.065 1552 Dihedral : 4.534 45.617 1255 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.41 % Favored : 96.24 % Rotamer: Outliers : 3.14 % Allowed : 28.45 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.86 % Twisted General : 0.09 % 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: 1.31 (0.26), residues: 1116 helix: 2.10 (0.26), residues: 398 sheet: 1.16 (0.31), residues: 303 loop : -0.58 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 47 HIS 0.004 0.001 HIS A 89 PHE 0.014 0.002 PHE A 239 TYR 0.013 0.001 TYR F 50 ARG 0.006 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 178 time to evaluate : 0.989 Fit side-chains REVERT: A 25 ASP cc_start: 0.6863 (m-30) cc_final: 0.6663 (m-30) REVERT: B 8 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7706 (mt-10) REVERT: B 29 LYS cc_start: 0.7917 (tttm) cc_final: 0.7588 (ttmm) REVERT: B 35 LYS cc_start: 0.8392 (mtmm) cc_final: 0.8149 (mttm) REVERT: C 29 LEU cc_start: 0.7454 (tp) cc_final: 0.7238 (tt) REVERT: C 120 SER cc_start: 0.8107 (m) cc_final: 0.7696 (p) REVERT: F 183 SER cc_start: 0.8262 (m) cc_final: 0.7949 (p) REVERT: F 205 LEU cc_start: 0.8150 (mt) cc_final: 0.7824 (mt) outliers start: 30 outliers final: 18 residues processed: 197 average time/residue: 0.2157 time to fit residues: 58.1359 Evaluate side-chains 186 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain F residue 125 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 228 ASN C 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9049 Z= 0.276 Angle : 0.601 16.155 12274 Z= 0.313 Chirality : 0.044 0.269 1391 Planarity : 0.004 0.062 1552 Dihedral : 4.699 31.271 1255 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.58 % Favored : 96.06 % Rotamer: Outliers : 4.29 % Allowed : 27.30 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.86 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1116 helix: 2.03 (0.26), residues: 398 sheet: 0.92 (0.30), residues: 301 loop : -0.70 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 47 HIS 0.004 0.001 HIS A 89 PHE 0.018 0.002 PHE C 273 TYR 0.011 0.001 TYR A 83 ARG 0.007 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 0.965 Fit side-chains REVERT: A 47 ARG cc_start: 0.8307 (mmt-90) cc_final: 0.8091 (mpt180) REVERT: A 153 ASN cc_start: 0.8184 (t0) cc_final: 0.7849 (t0) REVERT: B 35 LYS cc_start: 0.8345 (mtmm) cc_final: 0.8085 (mttm) REVERT: B 330 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7408 (mttt) REVERT: C 29 LEU cc_start: 0.7470 (tp) cc_final: 0.7240 (tt) REVERT: C 120 SER cc_start: 0.8230 (m) cc_final: 0.7797 (p) REVERT: C 175 VAL cc_start: 0.6227 (p) cc_final: 0.5976 (t) REVERT: F 125 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8460 (p) REVERT: F 183 SER cc_start: 0.8214 (m) cc_final: 0.7901 (p) REVERT: F 205 LEU cc_start: 0.8280 (mt) cc_final: 0.7916 (mt) outliers start: 41 outliers final: 25 residues processed: 199 average time/residue: 0.2301 time to fit residues: 61.7992 Evaluate side-chains 195 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.2980 chunk 52 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7315 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9049 Z= 0.235 Angle : 0.571 15.803 12274 Z= 0.298 Chirality : 0.043 0.281 1391 Planarity : 0.005 0.090 1552 Dihedral : 4.571 30.636 1255 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.49 % Favored : 96.15 % Rotamer: Outliers : 3.77 % Allowed : 28.97 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.02 (0.25), residues: 1116 helix: 2.06 (0.26), residues: 397 sheet: 0.71 (0.29), residues: 302 loop : -0.69 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 134 HIS 0.003 0.001 HIS B 244 PHE 0.016 0.002 PHE C 273 TYR 0.009 0.001 TYR F 50 ARG 0.007 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 0.975 Fit side-chains REVERT: A 153 ASN cc_start: 0.8231 (t0) cc_final: 0.7856 (t0) REVERT: B 35 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8073 (mttm) REVERT: B 330 LYS cc_start: 0.7650 (mtmt) cc_final: 0.7422 (mttt) REVERT: B 351 CYS cc_start: 0.6964 (p) cc_final: 0.6701 (m) REVERT: C 29 LEU cc_start: 0.7456 (tp) cc_final: 0.7247 (tt) REVERT: C 120 SER cc_start: 0.8269 (m) cc_final: 0.7872 (p) REVERT: C 175 VAL cc_start: 0.6420 (p) cc_final: 0.6213 (t) REVERT: F 125 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8447 (p) REVERT: F 183 SER cc_start: 0.8209 (m) cc_final: 0.7891 (p) REVERT: F 216 MET cc_start: 0.8353 (ptm) cc_final: 0.8134 (ttp) outliers start: 36 outliers final: 29 residues processed: 196 average time/residue: 0.2209 time to fit residues: 58.9022 Evaluate side-chains 196 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9049 Z= 0.267 Angle : 0.587 15.648 12274 Z= 0.305 Chirality : 0.044 0.279 1391 Planarity : 0.005 0.092 1552 Dihedral : 4.634 29.105 1255 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.85 % Favored : 95.79 % Rotamer: Outliers : 5.13 % Allowed : 29.08 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.93 (0.25), residues: 1116 helix: 2.01 (0.26), residues: 397 sheet: 0.60 (0.29), residues: 301 loop : -0.71 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 47 HIS 0.004 0.001 HIS B 244 PHE 0.019 0.002 PHE C 273 TYR 0.010 0.001 TYR A 83 ARG 0.006 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 168 time to evaluate : 0.953 Fit side-chains REVERT: A 153 ASN cc_start: 0.8317 (t0) cc_final: 0.8069 (t0) REVERT: A 157 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8316 (m) REVERT: B 35 LYS cc_start: 0.8327 (mtmm) cc_final: 0.8061 (mttm) REVERT: B 330 LYS cc_start: 0.7661 (mtmt) cc_final: 0.7415 (mttt) REVERT: C 120 SER cc_start: 0.8237 (m) cc_final: 0.7829 (p) REVERT: C 229 LEU cc_start: 0.7211 (tp) cc_final: 0.7002 (tp) REVERT: F 125 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8467 (p) REVERT: F 183 SER cc_start: 0.8201 (m) cc_final: 0.7885 (p) outliers start: 49 outliers final: 33 residues processed: 201 average time/residue: 0.2287 time to fit residues: 62.0936 Evaluate side-chains 199 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.7361 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9049 Z= 0.366 Angle : 0.636 15.555 12274 Z= 0.331 Chirality : 0.046 0.295 1391 Planarity : 0.005 0.089 1552 Dihedral : 4.943 33.528 1255 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.03 % Favored : 95.61 % Rotamer: Outliers : 5.13 % Allowed : 28.97 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.61 (0.25), residues: 1116 helix: 1.69 (0.26), residues: 407 sheet: 0.42 (0.29), residues: 303 loop : -0.89 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 47 HIS 0.005 0.001 HIS A 89 PHE 0.024 0.002 PHE C 273 TYR 0.012 0.002 TYR A 83 ARG 0.007 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 175 time to evaluate : 0.965 Fit side-chains REVERT: A 157 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8292 (m) REVERT: B 35 LYS cc_start: 0.8313 (mtmm) cc_final: 0.8055 (mttm) REVERT: B 330 LYS cc_start: 0.7694 (mtmt) cc_final: 0.7424 (mttt) REVERT: C 120 SER cc_start: 0.8257 (m) cc_final: 0.7874 (p) REVERT: C 136 MET cc_start: 0.6584 (mmt) cc_final: 0.6377 (mmm) REVERT: C 229 LEU cc_start: 0.7218 (tp) cc_final: 0.6994 (tp) REVERT: F 38 ARG cc_start: 0.8643 (ptt-90) cc_final: 0.8383 (ptt180) REVERT: F 125 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8571 (p) REVERT: F 183 SER cc_start: 0.8195 (m) cc_final: 0.7878 (p) outliers start: 49 outliers final: 40 residues processed: 208 average time/residue: 0.2438 time to fit residues: 67.2068 Evaluate side-chains 214 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7338 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9049 Z= 0.240 Angle : 0.587 15.418 12274 Z= 0.304 Chirality : 0.043 0.265 1391 Planarity : 0.005 0.087 1552 Dihedral : 4.729 30.615 1255 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.49 % Favored : 96.15 % Rotamer: Outliers : 4.60 % Allowed : 29.81 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.78 (0.25), residues: 1116 helix: 1.96 (0.26), residues: 401 sheet: 0.40 (0.29), residues: 301 loop : -0.80 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 134 HIS 0.004 0.001 HIS A 89 PHE 0.014 0.002 PHE C 273 TYR 0.009 0.001 TYR F 176 ARG 0.007 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 0.954 Fit side-chains REVERT: A 157 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8297 (m) REVERT: B 35 LYS cc_start: 0.8294 (mtmm) cc_final: 0.8034 (mttm) REVERT: B 330 LYS cc_start: 0.7658 (mtmt) cc_final: 0.7417 (mttt) REVERT: C 120 SER cc_start: 0.8207 (m) cc_final: 0.7822 (p) REVERT: C 229 LEU cc_start: 0.7238 (tp) cc_final: 0.7007 (tp) REVERT: F 183 SER cc_start: 0.8202 (m) cc_final: 0.7889 (p) outliers start: 44 outliers final: 38 residues processed: 195 average time/residue: 0.2128 time to fit residues: 57.1803 Evaluate side-chains 206 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 167 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 84 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.7334 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9049 Z= 0.227 Angle : 0.591 15.269 12274 Z= 0.303 Chirality : 0.042 0.251 1391 Planarity : 0.004 0.085 1552 Dihedral : 4.633 30.029 1255 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.85 % Favored : 95.79 % Rotamer: Outliers : 5.02 % Allowed : 29.39 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.83 (0.25), residues: 1116 helix: 2.00 (0.26), residues: 400 sheet: 0.40 (0.29), residues: 301 loop : -0.75 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 134 HIS 0.004 0.001 HIS A 89 PHE 0.014 0.002 PHE C 273 TYR 0.009 0.001 TYR F 60 ARG 0.007 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 0.920 Fit side-chains REVERT: A 144 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 157 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8316 (m) REVERT: B 35 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8049 (mttm) REVERT: B 330 LYS cc_start: 0.7645 (mtmt) cc_final: 0.7418 (mttt) REVERT: C 120 SER cc_start: 0.8232 (m) cc_final: 0.7868 (p) REVERT: F 183 SER cc_start: 0.8195 (m) cc_final: 0.7884 (p) outliers start: 48 outliers final: 39 residues processed: 195 average time/residue: 0.2183 time to fit residues: 58.7003 Evaluate side-chains 209 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.0040 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 0.0170 chunk 64 optimal weight: 0.8980 overall best weight: 0.3430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9049 Z= 0.169 Angle : 0.554 12.433 12274 Z= 0.284 Chirality : 0.041 0.225 1391 Planarity : 0.004 0.082 1552 Dihedral : 4.492 27.575 1255 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.05 % Favored : 96.59 % Rotamer: Outliers : 3.77 % Allowed : 31.17 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.94 (0.25), residues: 1116 helix: 2.18 (0.26), residues: 397 sheet: 0.43 (0.29), residues: 295 loop : -0.71 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 75 HIS 0.003 0.001 HIS F 35 PHE 0.013 0.001 PHE C 275 TYR 0.008 0.001 TYR F 221 ARG 0.007 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 0.921 Fit side-chains REVERT: A 144 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7462 (mm) REVERT: A 157 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8321 (m) REVERT: A 187 SER cc_start: 0.8046 (t) cc_final: 0.7769 (p) REVERT: B 35 LYS cc_start: 0.8319 (mtmm) cc_final: 0.8058 (mttm) REVERT: B 330 LYS cc_start: 0.7599 (mtmt) cc_final: 0.7369 (mttp) REVERT: C 120 SER cc_start: 0.8236 (m) cc_final: 0.7866 (p) REVERT: C 206 MET cc_start: 0.8156 (tpt) cc_final: 0.7953 (mmm) REVERT: F 183 SER cc_start: 0.8206 (m) cc_final: 0.7900 (p) outliers start: 36 outliers final: 30 residues processed: 198 average time/residue: 0.2263 time to fit residues: 60.4149 Evaluate side-chains 207 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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: 0.7333 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9049 Z= 0.246 Angle : 0.580 11.010 12274 Z= 0.296 Chirality : 0.043 0.215 1391 Planarity : 0.004 0.074 1552 Dihedral : 4.611 30.114 1255 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.94 % Favored : 95.88 % Rotamer: Outliers : 3.77 % Allowed : 31.59 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.88 (0.25), residues: 1116 helix: 2.07 (0.26), residues: 400 sheet: 0.37 (0.29), residues: 296 loop : -0.70 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 134 HIS 0.004 0.001 HIS A 89 PHE 0.014 0.002 PHE A 149 TYR 0.018 0.001 TYR F 221 ARG 0.007 0.000 ARG A 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 144 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7662 (mm) REVERT: A 157 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8328 (m) REVERT: A 187 SER cc_start: 0.8016 (t) cc_final: 0.7739 (p) REVERT: B 35 LYS cc_start: 0.8303 (mtmm) cc_final: 0.8054 (mttm) REVERT: B 330 LYS cc_start: 0.7627 (mtmt) cc_final: 0.7383 (mttp) REVERT: C 120 SER cc_start: 0.8263 (m) cc_final: 0.7887 (p) REVERT: C 206 MET cc_start: 0.8203 (tpt) cc_final: 0.7988 (mmm) REVERT: F 183 SER cc_start: 0.8195 (m) cc_final: 0.7895 (p) outliers start: 36 outliers final: 33 residues processed: 192 average time/residue: 0.2248 time to fit residues: 58.6644 Evaluate side-chains 209 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.115605 restraints weight = 12654.032| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.70 r_work: 0.3347 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9049 Z= 0.259 Angle : 0.572 10.274 12274 Z= 0.296 Chirality : 0.043 0.199 1391 Planarity : 0.004 0.080 1552 Dihedral : 4.692 31.070 1255 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.94 % Favored : 95.88 % Rotamer: Outliers : 3.97 % Allowed : 31.28 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.83 (0.25), residues: 1116 helix: 2.05 (0.26), residues: 400 sheet: 0.30 (0.29), residues: 301 loop : -0.72 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 134 HIS 0.004 0.001 HIS A 89 PHE 0.015 0.002 PHE C 273 TYR 0.012 0.001 TYR F 221 ARG 0.007 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.61 seconds wall clock time: 42 minutes 37.99 seconds (2557.99 seconds total)