Starting phenix.real_space_refine on Wed Jul 30 06:08:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpq_43413/07_2025/8vpq_43413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpq_43413/07_2025/8vpq_43413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vpq_43413/07_2025/8vpq_43413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpq_43413/07_2025/8vpq_43413.map" model { file = "/net/cci-nas-00/data/ceres_data/8vpq_43413/07_2025/8vpq_43413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpq_43413/07_2025/8vpq_43413.cif" } resolution = 3.3 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= 0.025 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 S 75 5.16 5 C 7665 2.51 5 N 2055 2.21 5 O 2288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12090 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3947 Classifications: {'peptide': 499} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 484} Chain breaks: 3 Chain: "B" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4001 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 13, 'TRANS': 492} Chain breaks: 1 Chain: "C" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2985 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Chain: "D" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1120 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.15, per 1000 atoms: 0.67 Number of scatterers: 12090 At special positions: 0 Unit cell: (77.28, 136.08, 154.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 75 16.00 P 6 15.00 O 2288 8.00 N 2055 7.00 C 7665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.87 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 600 " pdb="ZN ZN C 600 " - pdb=" ND1 HIS C 178 " 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 20 sheets defined 31.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.505A pdb=" N ARG A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.801A pdb=" N LEU A 79 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 111 through 120 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.866A pdb=" N ILE A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 159 through 162 Processing helix chain 'A' and resid 163 through 173 removed outlier: 3.912A pdb=" N TRP A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 189 removed outlier: 4.158A pdb=" N CYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.529A pdb=" N GLN A 219 " --> pdb=" O PRO A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.530A pdb=" N ALA A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'B' and resid 41 through 54 removed outlier: 3.879A pdb=" N ARG B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.632A pdb=" N LEU B 79 " --> pdb=" O HIS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 111 through 120 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.699A pdb=" N THR B 157 " --> pdb=" O PHE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 170 removed outlier: 3.509A pdb=" N MET B 167 " --> pdb=" O CYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.727A pdb=" N CYS B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'C' and resid 18 through 22 removed outlier: 3.913A pdb=" N ASN C 21 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR C 22 " --> pdb=" O VAL C 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 18 through 22' Processing helix chain 'C' and resid 32 through 43 removed outlier: 4.234A pdb=" N ARG C 36 " --> pdb=" O PRO C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 78 removed outlier: 3.511A pdb=" N ILE C 73 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 94 Processing helix chain 'C' and resid 106 through 125 Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 180 through 187 Processing helix chain 'C' and resid 233 through 253 removed outlier: 3.618A pdb=" N TYR C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Proline residue: C 243 - end of helix Processing helix chain 'C' and resid 277 through 290 removed outlier: 3.563A pdb=" N HIS C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 320 Processing helix chain 'C' and resid 356 through 371 Processing helix chain 'D' and resid 15 through 19 Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.683A pdb=" N SER D 23 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 24 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 55 Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 92 through 106 Processing helix chain 'D' and resid 109 through 114 Processing helix chain 'D' and resid 122 through 131 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.515A pdb=" N PHE B 469 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 127 removed outlier: 3.626A pdb=" N TYR B 35 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.821A pdb=" N SER A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE A 256 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 259 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 533 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS A 261 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU A 531 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 299 removed outlier: 4.527A pdb=" N LEU A 303 " --> pdb=" O CYS A 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 344 Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 356 removed outlier: 4.143A pdb=" N GLY A 355 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 390 through 394 removed outlier: 3.567A pdb=" N LYS A 427 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 404 through 406 Processing sheet with id=AB2, first strand: chain 'A' and resid 442 through 446 Processing sheet with id=AB3, first strand: chain 'A' and resid 485 through 489 Processing sheet with id=AB4, first strand: chain 'B' and resid 70 through 74 Processing sheet with id=AB5, first strand: chain 'B' and resid 268 through 271 removed outlier: 6.951A pdb=" N LYS B 261 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU B 531 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 295 through 299 Processing sheet with id=AB7, first strand: chain 'B' and resid 340 through 342 removed outlier: 3.544A pdb=" N ILE B 367 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 390 through 394 Processing sheet with id=AB9, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AC1, first strand: chain 'B' and resid 486 through 488 removed outlier: 4.121A pdb=" N ILE B 494 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 223 through 228 removed outlier: 7.924A pdb=" N VAL C 224 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR C 226 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER C 197 " --> pdb=" O TYR C 226 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU C 228 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS C 199 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 170 " --> pdb=" O MET C 194 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL C 196 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR C 172 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE C 198 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP C 174 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LYS C 200 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU C 171 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLN C 260 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE C 173 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL C 257 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU C 298 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU C 259 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA C 132 " --> pdb=" O MET C 297 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL C 11 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N TYR C 54 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR C 13 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 31 " --> pdb=" O ARG C 55 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 3.39 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: 3955 1.34 - 1.46: 2696 1.46 - 1.58: 5598 1.58 - 1.69: 6 1.69 - 1.81: 110 Bond restraints: 12365 Sorted by residual: bond pdb=" C5 IHP D 701 " pdb=" O15 IHP D 701 " ideal model delta sigma weight residual 1.389 1.443 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" C1 IHP D 701 " pdb=" O11 IHP D 701 " ideal model delta sigma weight residual 1.392 1.443 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" C3 IHP D 701 " pdb=" O13 IHP D 701 " ideal model delta sigma weight residual 1.393 1.443 -0.050 2.00e-02 2.50e+03 6.19e+00 bond pdb=" C6 IHP D 701 " pdb=" O16 IHP D 701 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" O15 IHP D 701 " pdb=" P5 IHP D 701 " ideal model delta sigma weight residual 1.675 1.626 0.049 2.00e-02 2.50e+03 5.99e+00 ... (remaining 12360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 16124 1.83 - 3.65: 564 3.65 - 5.48: 54 5.48 - 7.31: 12 7.31 - 9.14: 5 Bond angle restraints: 16759 Sorted by residual: angle pdb=" N ASN A 232 " pdb=" CA ASN A 232 " pdb=" C ASN A 232 " ideal model delta sigma weight residual 114.62 107.20 7.42 1.14e+00 7.69e-01 4.24e+01 angle pdb=" C LYS A 447 " pdb=" CA LYS A 447 " pdb=" CB LYS A 447 " ideal model delta sigma weight residual 117.23 110.75 6.48 1.36e+00 5.41e-01 2.27e+01 angle pdb=" CA GLN B 105 " pdb=" C GLN B 105 " pdb=" N ASP B 106 " ideal model delta sigma weight residual 119.56 116.87 2.69 5.80e-01 2.97e+00 2.15e+01 angle pdb=" C GLY C 338 " pdb=" N PRO C 339 " pdb=" CA PRO C 339 " ideal model delta sigma weight residual 119.84 124.54 -4.70 1.25e+00 6.40e-01 1.41e+01 angle pdb=" CA LYS A 447 " pdb=" C LYS A 447 " pdb=" N ASP A 448 " ideal model delta sigma weight residual 119.98 116.94 3.04 8.50e-01 1.38e+00 1.28e+01 ... (remaining 16754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 7035 15.24 - 30.47: 268 30.47 - 45.71: 56 45.71 - 60.94: 2 60.94 - 76.18: 8 Dihedral angle restraints: 7369 sinusoidal: 2957 harmonic: 4412 Sorted by residual: dihedral pdb=" CA ALA A 454 " pdb=" C ALA A 454 " pdb=" N GLU A 455 " pdb=" CA GLU A 455 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLY C 202 " pdb=" C GLY C 202 " pdb=" N GLU C 203 " pdb=" CA GLU C 203 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU B 314 " pdb=" C LEU B 314 " pdb=" N ARG B 315 " pdb=" CA ARG B 315 " ideal model delta harmonic sigma weight residual 180.00 -159.42 -20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 7366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1480 0.052 - 0.105: 302 0.105 - 0.157: 54 0.157 - 0.210: 2 0.210 - 0.262: 2 Chirality restraints: 1840 Sorted by residual: chirality pdb=" C1 IHP D 701 " pdb=" C2 IHP D 701 " pdb=" C6 IHP D 701 " pdb=" O11 IHP D 701 " both_signs ideal model delta sigma weight residual False 2.32 2.58 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3 IHP D 701 " pdb=" C2 IHP D 701 " pdb=" C4 IHP D 701 " pdb=" O13 IHP D 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.59 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C5 IHP D 701 " pdb=" C4 IHP D 701 " pdb=" C6 IHP D 701 " pdb=" O15 IHP D 701 " both_signs ideal model delta sigma weight residual False -2.42 -2.60 0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 1837 not shown) Planarity restraints: 2149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 332 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO B 333 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 333 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 333 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 351 " -0.016 2.00e-02 2.50e+03 1.33e-02 3.52e+00 pdb=" CG TYR B 351 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 351 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 351 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 351 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 351 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 351 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 351 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 431 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 432 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 432 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 432 " -0.025 5.00e-02 4.00e+02 ... (remaining 2146 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 113 2.61 - 3.18: 10618 3.18 - 3.75: 17167 3.75 - 4.33: 25121 4.33 - 4.90: 41772 Nonbonded interactions: 94791 Sorted by model distance: nonbonded pdb=" OD2 ASP C 176 " pdb="ZN ZN C 600 " model vdw 2.036 2.230 nonbonded pdb=" OH TYR B 351 " pdb=" OG1 THR B 423 " model vdw 2.103 3.040 nonbonded pdb=" OG SER A 468 " pdb=" OH TYR B 31 " model vdw 2.111 3.040 nonbonded pdb=" OE2 GLU A 149 " pdb=" OH TYR B 35 " model vdw 2.124 3.040 nonbonded pdb=" O HIS C 28 " pdb=" NZ LYS C 31 " model vdw 2.137 3.120 ... (remaining 94786 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 536) selection = (chain 'B' and (resid 26 through 93 or resid 99 through 307 or resid 312 through \ 476 or resid 483 through 536)) } 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: 4.840 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 32.130 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.004 0.058 12366 Z= 0.204 Angle : 0.787 9.135 16759 Z= 0.470 Chirality : 0.044 0.262 1840 Planarity : 0.004 0.054 2149 Dihedral : 9.419 76.178 4529 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 3.01 % Allowed : 13.80 % Favored : 83.19 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % 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: -4.85 (0.17), residues: 1493 helix: -3.21 (0.17), residues: 457 sheet: -2.89 (0.27), residues: 305 loop : -3.35 (0.19), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 485 HIS 0.006 0.001 HIS C 28 PHE 0.022 0.002 PHE B 153 TYR 0.031 0.002 TYR B 351 ARG 0.004 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.17518 ( 420) hydrogen bonds : angle 10.00653 ( 1140) metal coordination : bond 0.05137 ( 1) covalent geometry : bond 0.00405 (12365) covalent geometry : angle 0.78657 (16759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.397 Fit side-chains REVERT: A 89 MET cc_start: 0.7566 (ttm) cc_final: 0.7291 (ttm) REVERT: A 440 ARG cc_start: 0.7550 (tpp80) cc_final: 0.7336 (ttm-80) REVERT: A 498 ARG cc_start: 0.6907 (tpm-80) cc_final: 0.6620 (mpt180) REVERT: B 249 GLU cc_start: 0.7114 (tp30) cc_final: 0.6733 (tp30) REVERT: B 261 LYS cc_start: 0.7874 (ttmm) cc_final: 0.7583 (tttt) REVERT: B 356 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7856 (ttmm) REVERT: B 374 ASN cc_start: 0.6992 (m-40) cc_final: 0.6740 (m-40) REVERT: B 411 PHE cc_start: 0.6834 (m-80) cc_final: 0.6074 (m-10) REVERT: C 10 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8287 (ttpp) REVERT: C 18 ASP cc_start: 0.7197 (t0) cc_final: 0.6788 (t0) REVERT: C 48 TYR cc_start: 0.5157 (p90) cc_final: 0.4876 (p90) REVERT: C 221 TYR cc_start: 0.7951 (m-10) cc_final: 0.7695 (m-10) REVERT: C 253 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7674 (mt0) REVERT: D 60 MET cc_start: 0.5891 (tpt) cc_final: 0.5341 (tpp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2902 time to fit residues: 88.1742 Evaluate side-chains 124 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 134 optimal weight: 0.8980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 189 HIS A 201 HIS A 446 HIS ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 286 GLN B 287 ASN B 299 HIS B 395 ASN B 446 HIS C 40 ASN C 57 HIS ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.225502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.186813 restraints weight = 13805.865| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.51 r_work: 0.3869 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12366 Z= 0.146 Angle : 0.632 12.280 16759 Z= 0.327 Chirality : 0.045 0.173 1840 Planarity : 0.004 0.048 2149 Dihedral : 5.581 43.527 1685 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.50 % Favored : 91.69 % Rotamer: Outliers : 1.21 % Allowed : 6.68 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.35 (0.19), residues: 1493 helix: -1.33 (0.22), residues: 470 sheet: -2.17 (0.27), residues: 323 loop : -2.86 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 91 HIS 0.005 0.001 HIS C 140 PHE 0.016 0.002 PHE A 153 TYR 0.024 0.002 TYR B 351 ARG 0.006 0.001 ARG C 212 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 420) hydrogen bonds : angle 5.89294 ( 1140) metal coordination : bond 0.00071 ( 1) covalent geometry : bond 0.00342 (12365) covalent geometry : angle 0.63249 (16759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8059 (ttm) cc_final: 0.7680 (ttm) REVERT: A 404 GLU cc_start: 0.8269 (pt0) cc_final: 0.7933 (mt-10) REVERT: A 457 ASP cc_start: 0.7198 (t70) cc_final: 0.6655 (t0) REVERT: A 498 ARG cc_start: 0.7174 (tpm-80) cc_final: 0.6603 (mpt180) REVERT: B 217 CYS cc_start: 0.7834 (p) cc_final: 0.7086 (p) REVERT: B 347 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7505 (pttt) REVERT: B 411 PHE cc_start: 0.7181 (m-80) cc_final: 0.6482 (m-10) REVERT: C 10 LYS cc_start: 0.8620 (ttmt) cc_final: 0.7526 (tptt) REVERT: C 48 TYR cc_start: 0.6042 (p90) cc_final: 0.5635 (p90) REVERT: D 60 MET cc_start: 0.6739 (tpt) cc_final: 0.5978 (tpp) REVERT: D 130 TYR cc_start: 0.8137 (m-80) cc_final: 0.7850 (m-80) outliers start: 16 outliers final: 6 residues processed: 152 average time/residue: 0.2763 time to fit residues: 58.6162 Evaluate side-chains 120 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 177 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 106 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.206308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.173127 restraints weight = 13287.152| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 1.80 r_work: 0.3889 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12366 Z= 0.149 Angle : 0.578 7.685 16759 Z= 0.299 Chirality : 0.044 0.159 1840 Planarity : 0.004 0.048 2149 Dihedral : 5.293 43.186 1685 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.84 % Favored : 90.42 % Rotamer: Outliers : 1.44 % Allowed : 7.97 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.66 (0.20), residues: 1493 helix: -0.67 (0.24), residues: 471 sheet: -1.72 (0.28), residues: 325 loop : -2.56 (0.21), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 91 HIS 0.005 0.001 HIS A 429 PHE 0.019 0.002 PHE A 153 TYR 0.023 0.002 TYR B 351 ARG 0.005 0.000 ARG C 212 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 420) hydrogen bonds : angle 5.39394 ( 1140) metal coordination : bond 0.00087 ( 1) covalent geometry : bond 0.00355 (12365) covalent geometry : angle 0.57759 (16759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.662 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8186 (ttm) cc_final: 0.7777 (ttm) REVERT: A 313 MET cc_start: 0.6905 (tpp) cc_final: 0.6515 (tpt) REVERT: A 404 GLU cc_start: 0.8332 (pt0) cc_final: 0.8059 (mt-10) REVERT: A 457 ASP cc_start: 0.7295 (t70) cc_final: 0.6709 (t0) REVERT: B 347 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7609 (pttt) REVERT: B 411 PHE cc_start: 0.7273 (m-80) cc_final: 0.6452 (m-10) REVERT: C 10 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8425 (ttpp) REVERT: C 48 TYR cc_start: 0.6235 (p90) cc_final: 0.5846 (p90) REVERT: D 60 MET cc_start: 0.6932 (tpt) cc_final: 0.6202 (tpp) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 0.3056 time to fit residues: 56.5394 Evaluate side-chains 113 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 40 optimal weight: 0.0980 chunk 28 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.202927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.168289 restraints weight = 13080.978| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.16 r_work: 0.3759 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12366 Z= 0.132 Angle : 0.542 7.327 16759 Z= 0.281 Chirality : 0.043 0.156 1840 Planarity : 0.003 0.039 2149 Dihedral : 5.058 41.685 1685 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.83 % Favored : 92.50 % Rotamer: Outliers : 2.05 % Allowed : 8.50 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.17 (0.21), residues: 1493 helix: -0.24 (0.24), residues: 475 sheet: -1.43 (0.29), residues: 334 loop : -2.31 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 228 HIS 0.006 0.001 HIS A 429 PHE 0.012 0.001 PHE B 32 TYR 0.018 0.002 TYR B 351 ARG 0.004 0.000 ARG C 212 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 420) hydrogen bonds : angle 5.00062 ( 1140) metal coordination : bond 0.00087 ( 1) covalent geometry : bond 0.00315 (12365) covalent geometry : angle 0.54172 (16759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.878 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: A 89 MET cc_start: 0.8140 (ttm) cc_final: 0.7735 (ttm) REVERT: A 404 GLU cc_start: 0.8328 (pt0) cc_final: 0.8079 (mt-10) REVERT: A 448 ASP cc_start: 0.7684 (t0) cc_final: 0.7316 (t0) REVERT: A 457 ASP cc_start: 0.7306 (t70) cc_final: 0.6703 (t0) REVERT: B 217 CYS cc_start: 0.7737 (m) cc_final: 0.7521 (p) REVERT: B 347 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7579 (pttt) REVERT: B 411 PHE cc_start: 0.7304 (m-80) cc_final: 0.6824 (m-10) REVERT: C 10 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8437 (ttpp) REVERT: C 48 TYR cc_start: 0.6272 (p90) cc_final: 0.5878 (p90) REVERT: D 60 MET cc_start: 0.6964 (tpt) cc_final: 0.6373 (tpp) outliers start: 27 outliers final: 15 residues processed: 147 average time/residue: 0.3711 time to fit residues: 80.0624 Evaluate side-chains 133 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 101 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 146 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.207789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173713 restraints weight = 13139.585| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.87 r_work: 0.3896 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12366 Z= 0.113 Angle : 0.531 9.762 16759 Z= 0.272 Chirality : 0.043 0.152 1840 Planarity : 0.003 0.038 2149 Dihedral : 4.876 40.639 1685 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.50 % Favored : 93.03 % Rotamer: Outliers : 1.90 % Allowed : 8.80 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.21), residues: 1493 helix: 0.15 (0.25), residues: 469 sheet: -1.21 (0.30), residues: 319 loop : -2.20 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 132 HIS 0.006 0.001 HIS A 429 PHE 0.010 0.001 PHE B 437 TYR 0.014 0.001 TYR B 351 ARG 0.005 0.000 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 420) hydrogen bonds : angle 4.84318 ( 1140) metal coordination : bond 0.00017 ( 1) covalent geometry : bond 0.00262 (12365) covalent geometry : angle 0.53069 (16759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: A 89 MET cc_start: 0.8224 (ttm) cc_final: 0.7823 (ttm) REVERT: A 313 MET cc_start: 0.6789 (tpp) cc_final: 0.6382 (tpt) REVERT: A 448 ASP cc_start: 0.7748 (t0) cc_final: 0.7385 (t0) REVERT: A 457 ASP cc_start: 0.7287 (t70) cc_final: 0.6649 (t0) REVERT: A 466 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7827 (pp) REVERT: B 347 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7634 (pttt) REVERT: B 411 PHE cc_start: 0.7269 (m-80) cc_final: 0.6920 (m-10) REVERT: C 10 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8374 (ttpp) REVERT: C 48 TYR cc_start: 0.6253 (p90) cc_final: 0.5892 (p90) REVERT: D 60 MET cc_start: 0.7006 (tpt) cc_final: 0.6450 (tpp) REVERT: D 134 LYS cc_start: 0.6282 (mttp) cc_final: 0.5240 (pttp) outliers start: 25 outliers final: 17 residues processed: 143 average time/residue: 0.2688 time to fit residues: 55.7234 Evaluate side-chains 129 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.223766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.185763 restraints weight = 13917.371| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.46 r_work: 0.3837 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12366 Z= 0.127 Angle : 0.529 8.029 16759 Z= 0.272 Chirality : 0.043 0.152 1840 Planarity : 0.003 0.041 2149 Dihedral : 4.817 40.464 1685 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.70 % Favored : 92.83 % Rotamer: Outliers : 2.12 % Allowed : 9.33 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.65 (0.21), residues: 1493 helix: 0.27 (0.25), residues: 472 sheet: -1.04 (0.30), residues: 328 loop : -2.10 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 91 HIS 0.006 0.001 HIS A 429 PHE 0.011 0.001 PHE B 437 TYR 0.014 0.001 TYR B 462 ARG 0.004 0.000 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 420) hydrogen bonds : angle 4.72525 ( 1140) metal coordination : bond 0.00092 ( 1) covalent geometry : bond 0.00304 (12365) covalent geometry : angle 0.52900 (16759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 1.577 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: A 89 MET cc_start: 0.8081 (ttm) cc_final: 0.7702 (ttm) REVERT: A 313 MET cc_start: 0.6720 (tpp) cc_final: 0.6331 (tpt) REVERT: A 448 ASP cc_start: 0.7556 (t0) cc_final: 0.7274 (t0) REVERT: A 457 ASP cc_start: 0.7275 (t70) cc_final: 0.6649 (t0) REVERT: A 498 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7328 (ttm-80) REVERT: B 261 LYS cc_start: 0.8312 (mmtp) cc_final: 0.8027 (mmmm) REVERT: B 347 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7625 (pttt) REVERT: B 411 PHE cc_start: 0.7249 (m-80) cc_final: 0.6859 (m-10) REVERT: C 10 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8332 (ttpp) REVERT: D 134 LYS cc_start: 0.6375 (mttp) cc_final: 0.5458 (pttp) outliers start: 28 outliers final: 21 residues processed: 142 average time/residue: 0.3559 time to fit residues: 76.3345 Evaluate side-chains 140 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 334 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 12 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 38 optimal weight: 0.0030 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 86 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.200801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.167492 restraints weight = 13277.903| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 1.77 r_work: 0.3860 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12366 Z= 0.111 Angle : 0.518 7.017 16759 Z= 0.267 Chirality : 0.042 0.195 1840 Planarity : 0.003 0.039 2149 Dihedral : 4.697 39.833 1685 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.56 % Favored : 93.03 % Rotamer: Outliers : 2.50 % Allowed : 9.86 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.44 (0.22), residues: 1493 helix: 0.41 (0.25), residues: 473 sheet: -0.86 (0.30), residues: 328 loop : -1.99 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 91 HIS 0.006 0.001 HIS A 429 PHE 0.008 0.001 PHE A 497 TYR 0.011 0.001 TYR B 462 ARG 0.004 0.000 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 420) hydrogen bonds : angle 4.61482 ( 1140) metal coordination : bond 0.00019 ( 1) covalent geometry : bond 0.00254 (12365) covalent geometry : angle 0.51793 (16759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7455 (mp10) REVERT: A 89 MET cc_start: 0.8111 (ttm) cc_final: 0.7729 (ttm) REVERT: A 313 MET cc_start: 0.6717 (tpp) cc_final: 0.6314 (tpt) REVERT: A 448 ASP cc_start: 0.7548 (t0) cc_final: 0.7255 (t0) REVERT: A 457 ASP cc_start: 0.7268 (t70) cc_final: 0.6647 (t0) REVERT: A 498 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6427 (mtt90) REVERT: B 261 LYS cc_start: 0.8312 (mmtp) cc_final: 0.8014 (mmmm) REVERT: B 347 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7584 (pttt) REVERT: B 411 PHE cc_start: 0.7235 (m-80) cc_final: 0.6890 (m-10) REVERT: C 10 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8316 (ttpp) outliers start: 33 outliers final: 24 residues processed: 149 average time/residue: 0.2498 time to fit residues: 53.5556 Evaluate side-chains 145 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 334 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 0.0050 chunk 87 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS C 281 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.223954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.184874 restraints weight = 13825.313| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.52 r_work: 0.3863 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12366 Z= 0.124 Angle : 0.530 6.873 16759 Z= 0.272 Chirality : 0.043 0.150 1840 Planarity : 0.003 0.043 2149 Dihedral : 4.699 39.242 1685 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.63 % Favored : 92.97 % Rotamer: Outliers : 2.43 % Allowed : 10.24 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.22), residues: 1493 helix: 0.48 (0.25), residues: 474 sheet: -0.78 (0.31), residues: 313 loop : -1.96 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.006 0.001 HIS A 429 PHE 0.010 0.001 PHE B 437 TYR 0.013 0.001 TYR B 462 ARG 0.004 0.000 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 420) hydrogen bonds : angle 4.58950 ( 1140) metal coordination : bond 0.00039 ( 1) covalent geometry : bond 0.00296 (12365) covalent geometry : angle 0.53005 (16759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.508 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: A 89 MET cc_start: 0.8141 (ttm) cc_final: 0.7737 (ttm) REVERT: A 313 MET cc_start: 0.6799 (tpp) cc_final: 0.6428 (tpt) REVERT: A 437 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8062 (p90) REVERT: A 448 ASP cc_start: 0.7543 (t0) cc_final: 0.7274 (t0) REVERT: A 457 ASP cc_start: 0.7261 (t70) cc_final: 0.6641 (t0) REVERT: A 498 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6323 (mtt90) REVERT: A 533 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6085 (p90) REVERT: B 261 LYS cc_start: 0.8347 (mmtp) cc_final: 0.8042 (mmmm) REVERT: B 347 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7620 (pttt) REVERT: B 411 PHE cc_start: 0.7197 (m-80) cc_final: 0.6853 (m-10) REVERT: C 10 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8318 (ttpp) REVERT: C 330 TYR cc_start: 0.7541 (t80) cc_final: 0.7187 (t80) REVERT: D 60 MET cc_start: 0.6176 (tpt) cc_final: 0.4226 (tpp) REVERT: D 134 LYS cc_start: 0.6250 (mttp) cc_final: 0.5385 (pttp) outliers start: 32 outliers final: 24 residues processed: 144 average time/residue: 0.2587 time to fit residues: 54.1869 Evaluate side-chains 147 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 334 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 130 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 126 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 133 optimal weight: 0.0030 chunk 66 optimal weight: 0.1980 chunk 33 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.227594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.189915 restraints weight = 13696.787| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.26 r_work: 0.3914 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12366 Z= 0.093 Angle : 0.501 7.186 16759 Z= 0.259 Chirality : 0.042 0.213 1840 Planarity : 0.003 0.037 2149 Dihedral : 4.465 37.870 1685 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.89 % Favored : 93.70 % Rotamer: Outliers : 2.12 % Allowed : 11.00 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1493 helix: 0.69 (0.25), residues: 474 sheet: -0.85 (0.30), residues: 331 loop : -1.85 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 485 HIS 0.006 0.001 HIS A 429 PHE 0.008 0.001 PHE B 86 TYR 0.011 0.001 TYR C 48 ARG 0.004 0.000 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 420) hydrogen bonds : angle 4.42867 ( 1140) metal coordination : bond 0.00000 ( 1) covalent geometry : bond 0.00206 (12365) covalent geometry : angle 0.50060 (16759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7469 (mp10) REVERT: A 89 MET cc_start: 0.8107 (ttm) cc_final: 0.7728 (ttm) REVERT: A 313 MET cc_start: 0.6771 (tpp) cc_final: 0.6423 (tpt) REVERT: A 437 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8024 (p90) REVERT: A 457 ASP cc_start: 0.7235 (t70) cc_final: 0.6628 (t0) REVERT: A 498 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6432 (mtt90) REVERT: A 533 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6091 (p90) REVERT: B 261 LYS cc_start: 0.8291 (mmtp) cc_final: 0.8011 (mmmm) REVERT: B 411 PHE cc_start: 0.7190 (m-80) cc_final: 0.6935 (m-10) REVERT: C 10 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8333 (ttpp) REVERT: D 60 MET cc_start: 0.6051 (tpt) cc_final: 0.4200 (tpp) outliers start: 28 outliers final: 20 residues processed: 150 average time/residue: 0.2312 time to fit residues: 52.4335 Evaluate side-chains 139 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 334 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 118 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 129 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.226402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.191196 restraints weight = 13738.316| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.03 r_work: 0.3893 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12366 Z= 0.104 Angle : 0.513 7.986 16759 Z= 0.267 Chirality : 0.042 0.225 1840 Planarity : 0.003 0.039 2149 Dihedral : 4.420 36.640 1685 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.89 % Favored : 93.70 % Rotamer: Outliers : 1.90 % Allowed : 11.84 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.10 (0.22), residues: 1493 helix: 0.75 (0.25), residues: 476 sheet: -0.71 (0.30), residues: 330 loop : -1.82 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.006 0.001 HIS A 429 PHE 0.007 0.001 PHE C 252 TYR 0.012 0.001 TYR B 135 ARG 0.004 0.000 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 420) hydrogen bonds : angle 4.41132 ( 1140) metal coordination : bond 0.00030 ( 1) covalent geometry : bond 0.00237 (12365) covalent geometry : angle 0.51349 (16759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7698 (mm-40) REVERT: A 89 MET cc_start: 0.8119 (ttm) cc_final: 0.7737 (ttm) REVERT: A 313 MET cc_start: 0.6814 (tpp) cc_final: 0.6452 (tpt) REVERT: A 437 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8008 (p90) REVERT: A 457 ASP cc_start: 0.7231 (t70) cc_final: 0.6615 (t0) REVERT: A 498 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6416 (mtt90) REVERT: A 533 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6169 (p90) REVERT: B 261 LYS cc_start: 0.8286 (mmtp) cc_final: 0.8004 (mmmm) REVERT: B 411 PHE cc_start: 0.7197 (m-80) cc_final: 0.6901 (m-10) REVERT: C 10 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8338 (ttpp) REVERT: D 60 MET cc_start: 0.6103 (tpt) cc_final: 0.4359 (tpp) outliers start: 25 outliers final: 20 residues processed: 135 average time/residue: 0.2858 time to fit residues: 58.3826 Evaluate side-chains 137 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 334 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 0.5980 chunk 98 optimal weight: 0.0060 chunk 145 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.160841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.130502 restraints weight = 13695.929| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.38 r_work: 0.3245 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12366 Z= 0.225 Angle : 0.620 8.881 16759 Z= 0.317 Chirality : 0.046 0.220 1840 Planarity : 0.004 0.041 2149 Dihedral : 4.917 38.181 1685 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.70 % Favored : 91.90 % Rotamer: Outliers : 2.05 % Allowed : 11.76 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.40 (0.22), residues: 1493 helix: 0.36 (0.24), residues: 479 sheet: -0.71 (0.31), residues: 303 loop : -1.96 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 485 HIS 0.007 0.001 HIS A 429 PHE 0.014 0.002 PHE B 32 TYR 0.021 0.002 TYR B 135 ARG 0.004 0.000 ARG B 336 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 420) hydrogen bonds : angle 4.77297 ( 1140) metal coordination : bond 0.00256 ( 1) covalent geometry : bond 0.00555 (12365) covalent geometry : angle 0.62013 (16759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6888.12 seconds wall clock time: 124 minutes 52.93 seconds (7492.93 seconds total)