Starting phenix.real_space_refine on Wed Sep 17 23:09:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpq_43413/09_2025/8vpq_43413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpq_43413/09_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_43413/09_2025/8vpq_43413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpq_43413/09_2025/8vpq_43413.map" model { file = "/net/cci-nas-00/data/ceres_data/8vpq_43413/09_2025/8vpq_43413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpq_43413/09_2025/8vpq_43413.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.41, per 1000 atoms: 0.28 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: 0.82 Conformation dependent library (CDL) restraints added in 596.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.50 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: 2.08 Time building geometry restraints manager: 1.14 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: 5.170 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.380 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 156 TYR 0.031 0.002 TYR B 351 PHE 0.022 0.002 PHE B 153 TRP 0.023 0.002 TRP A 485 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00405 (12365) covalent geometry : angle 0.78657 (16759) hydrogen bonds : bond 0.17518 ( 420) hydrogen bonds : angle 10.00653 ( 1140) metal coordination : bond 0.05137 ( 1) *********************** 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 : 0.490 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: 0.1310 time to fit residues: 40.0702 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 : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS A 446 HIS B 34 ASN B 82 GLN B 286 GLN B 287 ASN B 299 HIS B 339 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.221955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.182993 restraints weight = 13806.677| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.54 r_work: 0.3711 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12366 Z= 0.190 Angle : 0.674 13.196 16759 Z= 0.347 Chirality : 0.047 0.180 1840 Planarity : 0.004 0.053 2149 Dihedral : 5.754 43.684 1685 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.90 % Favored : 91.29 % Rotamer: Outliers : 1.37 % Allowed : 7.06 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.44 (0.19), residues: 1493 helix: -1.45 (0.22), residues: 471 sheet: -2.29 (0.26), residues: 337 loop : -2.84 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 212 TYR 0.030 0.002 TYR B 351 PHE 0.020 0.002 PHE A 153 TRP 0.021 0.002 TRP D 91 HIS 0.005 0.001 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00462 (12365) covalent geometry : angle 0.67386 (16759) hydrogen bonds : bond 0.04434 ( 420) hydrogen bonds : angle 5.93713 ( 1140) metal coordination : bond 0.00099 ( 1) *********************** 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 152 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7976 (ttm) cc_final: 0.7572 (ttm) REVERT: A 404 GLU cc_start: 0.8258 (pt0) cc_final: 0.7929 (mt-10) REVERT: A 457 ASP cc_start: 0.7194 (t70) cc_final: 0.6640 (t0) REVERT: B 217 CYS cc_start: 0.7801 (p) cc_final: 0.7075 (p) REVERT: B 347 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7541 (pttt) REVERT: B 411 PHE cc_start: 0.7184 (m-80) cc_final: 0.6535 (m-10) REVERT: C 10 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8410 (ttpp) REVERT: C 253 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8194 (mt0) REVERT: D 130 TYR cc_start: 0.8178 (m-80) cc_final: 0.7865 (m-80) outliers start: 18 outliers final: 9 residues processed: 148 average time/residue: 0.1321 time to fit residues: 27.0685 Evaluate side-chains 122 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 155 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 366 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 101 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.222179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.182205 restraints weight = 13884.539| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.71 r_work: 0.3802 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12366 Z= 0.154 Angle : 0.582 7.325 16759 Z= 0.301 Chirality : 0.045 0.163 1840 Planarity : 0.004 0.049 2149 Dihedral : 5.359 43.441 1685 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.64 % Favored : 90.62 % Rotamer: Outliers : 1.67 % Allowed : 8.04 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.20), residues: 1493 helix: -0.69 (0.24), residues: 470 sheet: -1.75 (0.28), residues: 334 loop : -2.57 (0.21), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.024 0.002 TYR B 351 PHE 0.019 0.002 PHE A 153 TRP 0.012 0.001 TRP D 91 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00373 (12365) covalent geometry : angle 0.58179 (16759) hydrogen bonds : bond 0.03854 ( 420) hydrogen bonds : angle 5.37421 ( 1140) metal coordination : bond 0.00143 ( 1) *********************** 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 142 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8102 (ttm) cc_final: 0.7695 (ttm) REVERT: A 313 MET cc_start: 0.6846 (tpp) cc_final: 0.6453 (tpt) REVERT: A 404 GLU cc_start: 0.8260 (pt0) cc_final: 0.7996 (mt-10) REVERT: A 457 ASP cc_start: 0.7275 (t70) cc_final: 0.6679 (t0) REVERT: B 347 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7587 (pttt) REVERT: B 411 PHE cc_start: 0.7230 (m-80) cc_final: 0.6618 (m-10) REVERT: C 10 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8382 (ttpp) REVERT: C 221 TYR cc_start: 0.8011 (m-10) cc_final: 0.7800 (m-10) REVERT: C 253 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8184 (mt0) outliers start: 22 outliers final: 11 residues processed: 138 average time/residue: 0.1181 time to fit residues: 23.0592 Evaluate side-chains 123 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS 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 511 LEU 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 81 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4485 r_free = 0.4485 target = 0.221549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.182529 restraints weight = 13863.416| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.44 r_work: 0.3834 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12366 Z= 0.147 Angle : 0.563 6.884 16759 Z= 0.292 Chirality : 0.044 0.156 1840 Planarity : 0.004 0.041 2149 Dihedral : 5.199 42.154 1685 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.17 % Favored : 92.16 % Rotamer: Outliers : 1.82 % Allowed : 9.18 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.21), residues: 1493 helix: -0.37 (0.24), residues: 472 sheet: -1.53 (0.29), residues: 323 loop : -2.35 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.016 0.002 TYR B 351 PHE 0.011 0.001 PHE A 153 TRP 0.010 0.001 TRP D 34 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00353 (12365) covalent geometry : angle 0.56310 (16759) hydrogen bonds : bond 0.03615 ( 420) hydrogen bonds : angle 5.08874 ( 1140) metal coordination : bond 0.00048 ( 1) *********************** 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 146 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: A 89 MET cc_start: 0.8096 (ttm) cc_final: 0.7698 (ttm) REVERT: A 313 MET cc_start: 0.6835 (tpp) cc_final: 0.6479 (tpt) REVERT: A 404 GLU cc_start: 0.8195 (pt0) cc_final: 0.7968 (mt-10) REVERT: A 448 ASP cc_start: 0.7522 (t0) cc_final: 0.7187 (t0) REVERT: A 457 ASP cc_start: 0.7265 (t70) cc_final: 0.6666 (t0) REVERT: B 347 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7621 (pttt) REVERT: B 411 PHE cc_start: 0.7271 (m-80) cc_final: 0.6830 (m-10) REVERT: C 10 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8374 (ttpp) REVERT: C 253 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8156 (mt0) outliers start: 24 outliers final: 15 residues processed: 139 average time/residue: 0.1152 time to fit residues: 23.0847 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 : 0.403 ------------------------------------------------------------------------------- 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 A residue 531 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 122 VAL 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 90 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** 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 = 0.4450 r_free = 0.4450 target = 0.217574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.176522 restraints weight = 13883.732| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.95 r_work: 0.3598 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12366 Z= 0.227 Angle : 0.619 8.073 16759 Z= 0.318 Chirality : 0.046 0.172 1840 Planarity : 0.004 0.044 2149 Dihedral : 5.371 42.112 1685 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.57 % Favored : 90.89 % Rotamer: Outliers : 2.35 % Allowed : 9.56 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.21), residues: 1493 helix: -0.36 (0.24), residues: 476 sheet: -1.51 (0.29), residues: 335 loop : -2.29 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 440 TYR 0.017 0.002 TYR B 135 PHE 0.018 0.002 PHE A 153 TRP 0.011 0.001 TRP A 485 HIS 0.009 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00567 (12365) covalent geometry : angle 0.61868 (16759) hydrogen bonds : bond 0.04063 ( 420) hydrogen bonds : angle 5.15196 ( 1140) metal coordination : bond 0.00153 ( 1) *********************** 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 148 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.390 Fit side-chains REVERT: A 48 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: A 89 MET cc_start: 0.8115 (ttm) cc_final: 0.7727 (ttm) REVERT: A 404 GLU cc_start: 0.8367 (pt0) cc_final: 0.8136 (mt-10) REVERT: A 437 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.7980 (p90) REVERT: A 457 ASP cc_start: 0.7389 (t70) cc_final: 0.6779 (t0) REVERT: A 498 ARG cc_start: 0.7222 (tpm-80) cc_final: 0.6702 (ttm-80) REVERT: B 347 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7676 (pttt) REVERT: B 411 PHE cc_start: 0.7300 (m-80) cc_final: 0.6867 (m-10) REVERT: C 10 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8374 (ttpp) REVERT: C 253 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8169 (mt0) REVERT: C 334 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8079 (m-80) outliers start: 31 outliers final: 22 residues processed: 140 average time/residue: 0.1198 time to fit residues: 24.0923 Evaluate side-chains 142 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 531 LEU 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 347 LYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 334 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 81 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 96 optimal weight: 0.0470 chunk 35 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.221659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.182742 restraints weight = 13855.305| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.39 r_work: 0.3831 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12366 Z= 0.128 Angle : 0.538 10.230 16759 Z= 0.278 Chirality : 0.043 0.162 1840 Planarity : 0.003 0.043 2149 Dihedral : 5.038 41.154 1685 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.56 % Favored : 92.97 % Rotamer: Outliers : 1.90 % Allowed : 11.00 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.21), residues: 1493 helix: -0.03 (0.24), residues: 478 sheet: -1.27 (0.30), residues: 323 loop : -2.15 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 440 TYR 0.012 0.001 TYR B 462 PHE 0.013 0.001 PHE A 153 TRP 0.013 0.001 TRP D 91 HIS 0.006 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00306 (12365) covalent geometry : angle 0.53816 (16759) hydrogen bonds : bond 0.03382 ( 420) hydrogen bonds : angle 4.84528 ( 1140) metal coordination : bond 0.00044 ( 1) *********************** 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 154 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.353 Fit side-chains REVERT: A 48 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: A 89 MET cc_start: 0.8081 (ttm) cc_final: 0.7695 (ttm) REVERT: A 448 ASP cc_start: 0.7523 (t0) cc_final: 0.7200 (t0) REVERT: A 457 ASP cc_start: 0.7284 (t70) cc_final: 0.6680 (t0) REVERT: A 498 ARG cc_start: 0.7091 (tpm-80) cc_final: 0.6631 (ttm-80) REVERT: A 533 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.5990 (p90) REVERT: B 347 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7654 (pttt) REVERT: B 411 PHE cc_start: 0.7220 (m-80) cc_final: 0.6907 (m-10) REVERT: C 10 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8344 (ttpp) REVERT: C 253 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8135 (mt0) REVERT: C 330 TYR cc_start: 0.7429 (t80) cc_final: 0.7190 (t80) REVERT: D 60 MET cc_start: 0.6644 (tpt) cc_final: 0.6388 (tpt) REVERT: D 134 LYS cc_start: 0.6298 (mttp) cc_final: 0.5354 (pttp) outliers start: 25 outliers final: 20 residues processed: 144 average time/residue: 0.1145 time to fit residues: 23.6973 Evaluate side-chains 144 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 485 TRP Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 194 GLN 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 461 CYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.0050 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** 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 = 0.4464 r_free = 0.4464 target = 0.219105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.178931 restraints weight = 13833.394| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.62 r_work: 0.3808 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12366 Z= 0.182 Angle : 0.577 8.185 16759 Z= 0.297 Chirality : 0.045 0.164 1840 Planarity : 0.004 0.044 2149 Dihedral : 5.128 40.758 1685 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.90 % Favored : 91.69 % Rotamer: Outliers : 2.50 % Allowed : 10.77 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.21), residues: 1493 helix: -0.10 (0.24), residues: 484 sheet: -1.22 (0.29), residues: 323 loop : -2.13 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.015 0.002 TYR B 462 PHE 0.015 0.002 PHE A 153 TRP 0.011 0.001 TRP D 91 HIS 0.007 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00450 (12365) covalent geometry : angle 0.57739 (16759) hydrogen bonds : bond 0.03692 ( 420) hydrogen bonds : angle 4.90942 ( 1140) metal coordination : bond 0.00105 ( 1) *********************** 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 155 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.453 Fit side-chains REVERT: A 48 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7398 (mp10) REVERT: A 89 MET cc_start: 0.8085 (ttm) cc_final: 0.7750 (ttm) REVERT: A 437 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8007 (p90) REVERT: A 448 ASP cc_start: 0.7645 (t0) cc_final: 0.7442 (t0) REVERT: A 457 ASP cc_start: 0.7320 (t70) cc_final: 0.6743 (t0) REVERT: A 498 ARG cc_start: 0.7154 (tpm-80) cc_final: 0.6667 (ttm-80) REVERT: A 533 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.6303 (p90) REVERT: B 347 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7705 (pttt) REVERT: B 411 PHE cc_start: 0.7262 (m-80) cc_final: 0.6880 (m-10) REVERT: B 437 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8628 (p90) REVERT: C 10 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8311 (ttpp) REVERT: C 253 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8117 (mt0) REVERT: C 330 TYR cc_start: 0.7439 (t80) cc_final: 0.7182 (t80) REVERT: D 120 LYS cc_start: 0.6356 (ptmt) cc_final: 0.6010 (ptmt) outliers start: 33 outliers final: 23 residues processed: 143 average time/residue: 0.1107 time to fit residues: 23.0826 Evaluate side-chains 146 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 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 437 PHE Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 533 PHE 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 437 PHE 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 51 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.190328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.167570 restraints weight = 12564.642| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.05 r_work: 0.3336 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12366 Z= 0.143 Angle : 0.551 11.193 16759 Z= 0.283 Chirality : 0.043 0.154 1840 Planarity : 0.003 0.043 2149 Dihedral : 4.989 40.011 1685 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.83 % Favored : 92.77 % Rotamer: Outliers : 2.73 % Allowed : 10.55 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.21), residues: 1493 helix: 0.09 (0.24), residues: 485 sheet: -1.12 (0.30), residues: 313 loop : -2.06 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 440 TYR 0.012 0.001 TYR B 462 PHE 0.013 0.001 PHE A 153 TRP 0.011 0.001 TRP A 485 HIS 0.007 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00348 (12365) covalent geometry : angle 0.55142 (16759) hydrogen bonds : bond 0.03434 ( 420) hydrogen bonds : angle 4.77060 ( 1140) metal coordination : bond 0.00078 ( 1) *********************** 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 155 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.492 Fit side-chains REVERT: A 48 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: A 89 MET cc_start: 0.8112 (ttm) cc_final: 0.7723 (ttm) REVERT: A 337 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 437 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.7969 (p90) REVERT: A 448 ASP cc_start: 0.7487 (t0) cc_final: 0.7165 (t0) REVERT: A 457 ASP cc_start: 0.7132 (t70) cc_final: 0.6629 (t0) REVERT: A 498 ARG cc_start: 0.7174 (tpm-80) cc_final: 0.6711 (ttm-80) REVERT: A 533 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.6264 (p90) REVERT: B 347 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7626 (pttt) REVERT: B 411 PHE cc_start: 0.7065 (m-80) cc_final: 0.6768 (m-10) REVERT: C 10 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8381 (ttpp) REVERT: C 253 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8173 (mt0) REVERT: C 330 TYR cc_start: 0.7267 (t80) cc_final: 0.7059 (t80) outliers start: 36 outliers final: 28 residues processed: 141 average time/residue: 0.1025 time to fit residues: 21.9305 Evaluate side-chains 146 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 247 LEU Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 337 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 531 LEU 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 194 GLN 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 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 45 TYR Chi-restraints excluded: chain C residue 51 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 59 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 111 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.161544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.131170 restraints weight = 13783.382| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.43 r_work: 0.3256 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12366 Z= 0.154 Angle : 0.565 10.312 16759 Z= 0.290 Chirality : 0.044 0.225 1840 Planarity : 0.003 0.044 2149 Dihedral : 4.986 39.664 1685 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.37 % Favored : 92.23 % Rotamer: Outliers : 2.81 % Allowed : 10.55 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.21), residues: 1493 helix: 0.21 (0.24), residues: 480 sheet: -1.03 (0.30), residues: 313 loop : -2.03 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.013 0.001 TYR B 462 PHE 0.014 0.001 PHE A 153 TRP 0.011 0.001 TRP A 485 HIS 0.006 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00377 (12365) covalent geometry : angle 0.56451 (16759) hydrogen bonds : bond 0.03495 ( 420) hydrogen bonds : angle 4.75582 ( 1140) metal coordination : bond 0.00049 ( 1) *********************** 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 153 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.327 Fit side-chains REVERT: A 48 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7512 (mp10) REVERT: A 89 MET cc_start: 0.8230 (ttm) cc_final: 0.7841 (ttm) REVERT: A 337 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8313 (mp) REVERT: A 437 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.7953 (p90) REVERT: A 448 ASP cc_start: 0.7640 (t0) cc_final: 0.7273 (t0) REVERT: A 457 ASP cc_start: 0.7200 (t70) cc_final: 0.6692 (t0) REVERT: A 498 ARG cc_start: 0.7230 (tpm-80) cc_final: 0.6714 (ttm-80) REVERT: A 533 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.6301 (p90) REVERT: B 347 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7688 (pttt) REVERT: B 411 PHE cc_start: 0.7125 (m-80) cc_final: 0.6756 (m-10) REVERT: B 472 LEU cc_start: 0.8637 (mp) cc_final: 0.8430 (tt) REVERT: C 10 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8432 (ttpp) REVERT: C 253 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8190 (mt0) REVERT: C 330 TYR cc_start: 0.7390 (t80) cc_final: 0.7123 (t80) outliers start: 37 outliers final: 30 residues processed: 140 average time/residue: 0.1018 time to fit residues: 21.6817 Evaluate side-chains 149 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 247 LEU Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 337 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 531 LEU 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 194 GLN Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 394 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 12 CYS Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 51 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** 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 = 0.4130 r_free = 0.4130 target = 0.188745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.168287 restraints weight = 12716.861| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 0.92 r_work: 0.3336 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12366 Z= 0.181 Angle : 0.584 9.869 16759 Z= 0.299 Chirality : 0.045 0.217 1840 Planarity : 0.004 0.043 2149 Dihedral : 5.056 39.652 1685 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.17 % Favored : 92.43 % Rotamer: Outliers : 2.66 % Allowed : 10.93 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.21), residues: 1493 helix: 0.17 (0.24), residues: 481 sheet: -1.05 (0.30), residues: 313 loop : -2.03 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.015 0.002 TYR B 462 PHE 0.015 0.001 PHE A 153 TRP 0.012 0.001 TRP A 485 HIS 0.007 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00448 (12365) covalent geometry : angle 0.58445 (16759) hydrogen bonds : bond 0.03653 ( 420) hydrogen bonds : angle 4.79994 ( 1140) metal coordination : bond 0.00213 ( 1) ********************** 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 151 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.428 Fit side-chains REVERT: A 48 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: A 89 MET cc_start: 0.8136 (ttm) cc_final: 0.7772 (ttm) REVERT: A 337 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8313 (mp) REVERT: A 437 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8002 (p90) REVERT: A 448 ASP cc_start: 0.7567 (t0) cc_final: 0.7189 (t0) REVERT: A 457 ASP cc_start: 0.7165 (t70) cc_final: 0.6673 (t0) REVERT: A 498 ARG cc_start: 0.7160 (tpm-80) cc_final: 0.6717 (ttm-80) REVERT: A 533 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.6384 (p90) REVERT: B 347 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7705 (pttt) REVERT: B 411 PHE cc_start: 0.7075 (m-80) cc_final: 0.6770 (m-10) REVERT: C 330 TYR cc_start: 0.7276 (t80) cc_final: 0.7028 (t80) REVERT: D 60 MET cc_start: 0.7384 (tpt) cc_final: 0.5195 (tpt) outliers start: 35 outliers final: 29 residues processed: 140 average time/residue: 0.1043 time to fit residues: 22.2143 Evaluate side-chains 148 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 247 LEU Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 337 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 531 LEU 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 359 GLN Chi-restraints excluded: chain B residue 394 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 12 CYS Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 51 MET 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 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 128 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.189960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.165471 restraints weight = 12663.742| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.21 r_work: 0.3288 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12366 Z= 0.151 Angle : 0.560 9.379 16759 Z= 0.287 Chirality : 0.044 0.204 1840 Planarity : 0.003 0.043 2149 Dihedral : 4.966 39.194 1685 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.17 % Favored : 92.43 % Rotamer: Outliers : 2.88 % Allowed : 11.00 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.21), residues: 1493 helix: 0.31 (0.24), residues: 480 sheet: -0.93 (0.30), residues: 309 loop : -1.97 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.013 0.001 TYR B 462 PHE 0.014 0.001 PHE A 153 TRP 0.012 0.001 TRP A 485 HIS 0.007 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00369 (12365) covalent geometry : angle 0.56025 (16759) hydrogen bonds : bond 0.03484 ( 420) hydrogen bonds : angle 4.73375 ( 1140) metal coordination : bond 0.00106 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2957.67 seconds wall clock time: 51 minutes 43.66 seconds (3103.66 seconds total)