Starting phenix.real_space_refine on Thu Aug 6 14:32:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hjm_52218/08_2026/9hjm_52218.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hjm_52218/08_2026/9hjm_52218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hjm_52218/08_2026/9hjm_52218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hjm_52218/08_2026/9hjm_52218.map" model { file = "/net/cci-nas-00/data/ceres_data/9hjm_52218/08_2026/9hjm_52218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hjm_52218/08_2026/9hjm_52218.cif" } resolution = 3.24 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= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 9797 2.51 5 N 2555 2.21 5 O 2883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15297 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3102 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 15, 'TRANS': 377} Chain breaks: 1 Chain: "G" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 24, 'TRANS': 414} Chain: "H" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3268 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain: "I" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1218 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "J" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1418 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.64, per 1000 atoms: 0.17 Number of scatterers: 15297 At special positions: 0 Unit cell: (102.48, 104.16, 187.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2883 8.00 N 2555 7.00 C 9797 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 560.5 milliseconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3530 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 23 sheets defined 9.5% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'F' and resid 38 through 43 Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 76 through 81 removed outlier: 3.725A pdb=" N SER F 81 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 186 removed outlier: 4.541A pdb=" N GLY G 177 " --> pdb=" O PRO G 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 185 " --> pdb=" O TYR G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 201 Processing helix chain 'G' and resid 261 through 266 removed outlier: 3.624A pdb=" N LEU G 265 " --> pdb=" O ILE G 261 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN G 266 " --> pdb=" O SER G 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 261 through 266' Processing helix chain 'G' and resid 287 through 293 removed outlier: 3.757A pdb=" N PHE G 291 " --> pdb=" O SER G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 345 removed outlier: 3.821A pdb=" N PHE G 343 " --> pdb=" O VAL G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 384 removed outlier: 3.538A pdb=" N LEU G 378 " --> pdb=" O ILE G 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 removed outlier: 4.111A pdb=" N LEU H 56 " --> pdb=" O ASN H 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU H 57 " --> pdb=" O PRO H 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 57' Processing helix chain 'H' and resid 284 through 287 Processing helix chain 'H' and resid 399 through 404 Processing helix chain 'H' and resid 407 through 411 Processing helix chain 'I' and resid 32 through 49 removed outlier: 3.772A pdb=" N ALA I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP I 48 " --> pdb=" O ASN I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 130 Processing helix chain 'I' and resid 143 through 148 Processing helix chain 'J' and resid 33 through 48 removed outlier: 3.662A pdb=" N ASN J 48 " --> pdb=" O GLU J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.556A pdb=" N VAL J 155 " --> pdb=" O ASP J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 161 Processing helix chain 'J' and resid 162 through 165 Processing helix chain 'J' and resid 177 through 181 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 834 through 838 Processing sheet with id=AA1, first strand: chain 'F' and resid 47 through 48 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 47 through 48 current: chain 'F' and resid 107 through 114 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 107 through 114 current: chain 'F' and resid 129 through 149 removed outlier: 5.507A pdb=" N MET F 130 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY F 175 " --> pdb=" O MET F 130 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA F 132 " --> pdb=" O GLY F 173 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY F 173 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL F 134 " --> pdb=" O TYR F 171 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR F 171 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP F 169 " --> pdb=" O PRO F 136 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE F 192 " --> pdb=" O ASN F 168 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 191 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 201 " --> pdb=" O PRO F 211 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 238 through 247 current: chain 'F' and resid 272 through 285 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 272 through 285 current: chain 'F' and resid 301 through 310 removed outlier: 4.559A pdb=" N ILE F 328 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU F 412 " --> pdb=" O LEU F 403 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 323 through 324 Processing sheet with id=AA3, first strand: chain 'G' and resid 39 through 45 removed outlier: 6.430A pdb=" N MET G 450 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE G 307 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR G 452 " --> pdb=" O TRP G 305 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TRP G 305 " --> pdb=" O TYR G 452 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 47 through 52 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 280 through 286 current: chain 'G' and resid 357 through 358 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 357 through 358 current: chain 'G' and resid 419 through 425 Processing sheet with id=AA5, first strand: chain 'G' and resid 63 through 70 removed outlier: 8.862A pdb=" N LEU G 64 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR G 80 " --> pdb=" O LEU G 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 74 through 82 current: chain 'G' and resid 151 through 158 Processing sheet with id=AA6, first strand: chain 'G' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'G' and resid 272 through 275 Processing sheet with id=AA8, first strand: chain 'G' and resid 313 through 315 Processing sheet with id=AA9, first strand: chain 'G' and resid 386 through 389 removed outlier: 3.621A pdb=" N THR G 389 " --> pdb=" O LYS G 393 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS G 393 " --> pdb=" O THR G 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 43 through 50 removed outlier: 3.518A pdb=" N ARG H 45 " --> pdb=" O VAL H 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 62 through 64 removed outlier: 4.536A pdb=" N LEU H 98 " --> pdb=" O TRP H 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 153 through 158 removed outlier: 4.750A pdb=" N ILE H 445 " --> pdb=" O LEU H 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 172 through 176 Processing sheet with id=AB5, first strand: chain 'H' and resid 217 through 220 Processing sheet with id=AB6, first strand: chain 'H' and resid 252 through 258 removed outlier: 7.479A pdb=" N VAL H 252 " --> pdb=" O GLU H 273 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU H 273 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA H 269 " --> pdb=" O LEU H 256 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU H 292 " --> pdb=" O PHE H 280 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR H 282 " --> pdb=" O TRP H 290 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TRP H 290 " --> pdb=" O THR H 282 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 299 through 301 removed outlier: 6.665A pdb=" N VAL H 322 " --> pdb=" O VAL H 300 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 304 through 310 Processing sheet with id=AB9, first strand: chain 'H' and resid 359 through 363 Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 55 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 64 through 66 current: chain 'I' and resid 98 through 101 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 98 through 101 current: chain 'I' and resid 169 through 178 Processing sheet with id=AC2, first strand: chain 'J' and resid 54 through 56 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 77 through 82 current: chain 'J' and resid 112 through 115 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 112 through 115 current: chain 'J' and resid 137 through 143 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 137 through 143 current: chain 'J' and resid 191 through 201 Processing sheet with id=AC3, first strand: chain 'A' and resid 506 through 507 Processing sheet with id=AC4, first strand: chain 'A' and resid 514 through 518 removed outlier: 3.554A pdb=" N SER A 663 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 676 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS A 714 " --> pdb=" O GLY A 748 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TYR A 801 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TRP A 832 " --> pdb=" O TYR A 801 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ARG A 803 " --> pdb=" O ASN A 830 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASN A 830 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N THR A 805 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA A 828 " --> pdb=" O THR A 805 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLU A 807 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA A 826 " --> pdb=" O GLU A 807 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ARG A 809 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA A 824 " --> pdb=" O ARG A 809 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU A 822 " --> pdb=" O PRO A 811 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 819 " --> pdb=" O THR A 854 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 761 through 763 450 hydrogen bonds defined for protein. 1170 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: 2.49 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2480 1.31 - 1.44: 4508 1.44 - 1.57: 8579 1.57 - 1.70: 1 1.70 - 1.83: 115 Bond restraints: 15683 Sorted by residual: bond pdb=" CG LEU I 93 " pdb=" CD2 LEU I 93 " ideal model delta sigma weight residual 1.521 1.308 0.213 3.30e-02 9.18e+02 4.17e+01 bond pdb=" CD2 TYR I 46 " pdb=" CE2 TYR I 46 " ideal model delta sigma weight residual 1.382 1.247 0.135 3.00e-02 1.11e+03 2.03e+01 bond pdb=" CG ASN F 388 " pdb=" ND2 ASN F 388 " ideal model delta sigma weight residual 1.328 1.247 0.081 2.10e-02 2.27e+03 1.50e+01 bond pdb=" CG TYR I 46 " pdb=" CD2 TYR I 46 " ideal model delta sigma weight residual 1.389 1.310 0.079 2.10e-02 2.27e+03 1.41e+01 bond pdb=" C16 Z41 G 502 " pdb=" O2 Z41 G 502 " ideal model delta sigma weight residual 1.332 1.405 -0.073 2.00e-02 2.50e+03 1.32e+01 ... (remaining 15678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 21145 4.15 - 8.31: 77 8.31 - 12.46: 9 12.46 - 16.62: 0 16.62 - 20.77: 1 Bond angle restraints: 21232 Sorted by residual: angle pdb=" CB MET H 127 " pdb=" CG MET H 127 " pdb=" SD MET H 127 " ideal model delta sigma weight residual 112.70 91.93 20.77 3.00e+00 1.11e-01 4.79e+01 angle pdb=" CA MET H 127 " pdb=" CB MET H 127 " pdb=" CG MET H 127 " ideal model delta sigma weight residual 114.10 124.83 -10.73 2.00e+00 2.50e-01 2.88e+01 angle pdb=" C MET F 280 " pdb=" N ASP F 281 " pdb=" CA ASP F 281 " ideal model delta sigma weight residual 122.61 129.73 -7.12 1.56e+00 4.11e-01 2.09e+01 angle pdb=" CB GLU J 39 " pdb=" CG GLU J 39 " pdb=" CD GLU J 39 " ideal model delta sigma weight residual 112.60 105.41 7.19 1.70e+00 3.46e-01 1.79e+01 angle pdb=" CG MET H 127 " pdb=" SD MET H 127 " pdb=" CE MET H 127 " ideal model delta sigma weight residual 100.90 110.06 -9.16 2.20e+00 2.07e-01 1.73e+01 ... (remaining 21227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8636 17.94 - 35.88: 507 35.88 - 53.82: 94 53.82 - 71.76: 11 71.76 - 89.71: 7 Dihedral angle restraints: 9255 sinusoidal: 3699 harmonic: 5556 Sorted by residual: dihedral pdb=" CA TYR G 230 " pdb=" C TYR G 230 " pdb=" N LYS G 231 " pdb=" CA LYS G 231 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ASN F 265 " pdb=" C ASN F 265 " pdb=" N GLY F 266 " pdb=" CA GLY F 266 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR F 117 " pdb=" C TYR F 117 " pdb=" N PHE F 118 " pdb=" CA PHE F 118 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 9252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 2253 0.178 - 0.356: 12 0.356 - 0.534: 0 0.534 - 0.712: 0 0.712 - 0.890: 1 Chirality restraints: 2266 Sorted by residual: chirality pdb=" CG LEU I 93 " pdb=" CB LEU I 93 " pdb=" CD1 LEU I 93 " pdb=" CD2 LEU I 93 " both_signs ideal model delta sigma weight residual False -2.59 -1.70 -0.89 2.00e-01 2.50e+01 1.98e+01 chirality pdb=" CB ILE A 504 " pdb=" CA ILE A 504 " pdb=" CG1 ILE A 504 " pdb=" CG2 ILE A 504 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CG LEU J 90 " pdb=" CB LEU J 90 " pdb=" CD1 LEU J 90 " pdb=" CD2 LEU J 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 2263 not shown) Planarity restraints: 2725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 645 " -0.009 2.00e-02 2.50e+03 3.81e-02 2.54e+01 pdb=" CG PHE A 645 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE A 645 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 PHE A 645 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A 645 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 PHE A 645 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 645 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 52 " 0.035 2.00e-02 2.50e+03 3.20e-02 1.79e+01 pdb=" CG PHE I 52 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE I 52 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE I 52 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE I 52 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE I 52 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE I 52 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 845 " 0.351 9.50e-02 1.11e+02 1.57e-01 1.52e+01 pdb=" NE ARG A 845 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 845 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 845 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 845 " 0.011 2.00e-02 2.50e+03 ... (remaining 2722 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 83 2.51 - 3.11: 11046 3.11 - 3.71: 21760 3.71 - 4.30: 31749 4.30 - 4.90: 54825 Nonbonded interactions: 119463 Sorted by model distance: nonbonded pdb=" OE1 GLU J 39 " pdb=" OG1 THR J 191 " model vdw 1.915 3.040 nonbonded pdb=" OE2 GLU F 103 " pdb=" OG SER G 29 " model vdw 2.145 3.040 nonbonded pdb=" O SER G 236 " pdb=" OG1 THR G 237 " model vdw 2.175 3.040 nonbonded pdb=" OG SER F 95 " pdb=" OE2 GLU F 116 " model vdw 2.249 3.040 nonbonded pdb=" O VAL J 159 " pdb=" OH TYR J 199 " model vdw 2.253 3.040 ... (remaining 119458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.650 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.280 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 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 : 0.005 0.213 15685 Z= 0.223 Angle : 0.798 20.771 21232 Z= 0.418 Chirality : 0.054 0.890 2266 Planarity : 0.007 0.157 2725 Dihedral : 11.984 89.706 5725 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.04 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -1.33 (0.19), residues: 1902 helix: -0.67 (0.44), residues: 134 sheet: 0.06 (0.18), residues: 844 loop : -1.85 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 45 TYR 0.034 0.002 TYR H 148 PHE 0.072 0.003 PHE A 645 TRP 0.035 0.002 TRP A 534 HIS 0.011 0.001 HIS H 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (15683) covalent geometry : angle 0.79823 / 0.42 (21232) hydrogen bonds : bond 0.13959 / 8.70 ( 450) hydrogen bonds : angle 6.15176 / 4.10 ( 1170) Misc. bond : bond 0.05710 / 2.80 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: G 229 SER cc_start: 0.7845 (t) cc_final: 0.7379 (m) REVERT: H 86 MET cc_start: 0.6747 (ptm) cc_final: 0.6520 (ptp) REVERT: H 127 MET cc_start: 0.7203 (ttt) cc_final: 0.6832 (tpt) REVERT: H 334 ILE cc_start: 0.8521 (pt) cc_final: 0.8230 (pt) REVERT: I 36 ARG cc_start: 0.7474 (mtm180) cc_final: 0.7154 (mtp180) REVERT: I 85 GLU cc_start: 0.8212 (pm20) cc_final: 0.7850 (pm20) REVERT: I 145 TYR cc_start: 0.7060 (p90) cc_final: 0.6749 (p90) REVERT: J 186 TYR cc_start: 0.8045 (t80) cc_final: 0.7637 (t80) REVERT: A 552 THR cc_start: 0.6485 (m) cc_final: 0.6213 (m) REVERT: A 743 GLU cc_start: 0.8443 (pt0) cc_final: 0.8233 (pt0) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1026 time to fit residues: 29.6834 Evaluate side-chains 153 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.5266 > 50:) chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 149 GLN F 166 ASN F 388 ASN G 83 GLN G 254 ASN G 290 GLN H 42 GLN H 167 ASN I 37 HIS ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 646 GLN A 700 GLN A 793 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094166 restraints weight = 21178.289| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.41 r_work: 0.2986 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15685 Z= 0.163 Angle : 0.593 7.158 21232 Z= 0.314 Chirality : 0.046 0.185 2266 Planarity : 0.004 0.038 2725 Dihedral : 6.012 57.419 2152 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 92.01 % Rotamer: Outliers : 0.60 % Allowed : 6.10 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.19), residues: 1902 helix: -0.45 (0.44), residues: 135 sheet: 0.02 (0.18), residues: 824 loop : -1.79 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 45 TYR 0.020 0.001 TYR G 220 PHE 0.034 0.002 PHE A 645 TRP 0.024 0.001 TRP I 144 HIS 0.004 0.001 HIS H 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (15683) covalent geometry : angle 0.59264 / 0.31 (21232) hydrogen bonds : bond 0.03592 / 2.29 ( 450) hydrogen bonds : angle 5.28813 / 3.49 ( 1170) Misc. bond : bond 0.00086 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: F 280 MET cc_start: 0.8007 (mpp) cc_final: 0.7733 (mmm) REVERT: G 98 ASP cc_start: 0.8177 (t0) cc_final: 0.7890 (t70) REVERT: H 127 MET cc_start: 0.7628 (ttt) cc_final: 0.7234 (tpt) REVERT: H 225 ARG cc_start: 0.8758 (ttm170) cc_final: 0.8350 (ttm170) REVERT: H 334 ILE cc_start: 0.8554 (pt) cc_final: 0.8059 (mt) REVERT: H 446 TRP cc_start: 0.9063 (m100) cc_final: 0.8303 (m100) REVERT: J 186 TYR cc_start: 0.8022 (t80) cc_final: 0.7607 (t80) REVERT: A 705 SER cc_start: 0.7320 (t) cc_final: 0.6987 (p) REVERT: A 743 GLU cc_start: 0.8416 (pt0) cc_final: 0.8124 (pt0) outliers start: 10 outliers final: 7 residues processed: 169 average time/residue: 0.1143 time to fit residues: 28.2576 Evaluate side-chains 147 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain I residue 46 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 6 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 98 optimal weight: 0.0570 chunk 74 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 149 GLN ** F 388 ASN ** 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 = 0.3690 r_free = 0.3690 target = 0.139183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.096127 restraints weight = 21304.207| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.45 r_work: 0.3015 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15685 Z= 0.101 Angle : 0.514 6.542 21232 Z= 0.272 Chirality : 0.043 0.149 2266 Planarity : 0.003 0.037 2725 Dihedral : 5.631 57.540 2152 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.52 % Favored : 93.38 % Rotamer: Outliers : 1.03 % Allowed : 7.54 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -1.18 (0.19), residues: 1902 helix: -0.36 (0.44), residues: 140 sheet: 0.19 (0.19), residues: 808 loop : -1.76 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 179 TYR 0.013 0.001 TYR H 427 PHE 0.017 0.001 PHE A 645 TRP 0.011 0.001 TRP I 144 HIS 0.003 0.001 HIS H 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (15683) covalent geometry : angle 0.51408 / 0.27 (21232) hydrogen bonds : bond 0.03000 / 1.91 ( 450) hydrogen bonds : angle 4.95703 / 3.28 ( 1170) Misc. bond : bond 0.00008 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: G 98 ASP cc_start: 0.8133 (t0) cc_final: 0.7894 (t70) REVERT: G 147 ASP cc_start: 0.7711 (m-30) cc_final: 0.7332 (m-30) REVERT: H 127 MET cc_start: 0.7824 (ttt) cc_final: 0.7382 (tpt) REVERT: H 225 ARG cc_start: 0.8719 (ttm170) cc_final: 0.8334 (ttm170) REVERT: H 334 ILE cc_start: 0.8536 (pt) cc_final: 0.8005 (mt) REVERT: H 446 TRP cc_start: 0.9036 (m100) cc_final: 0.8330 (m100) REVERT: J 186 TYR cc_start: 0.7992 (t80) cc_final: 0.7568 (t80) REVERT: A 705 SER cc_start: 0.7430 (t) cc_final: 0.7113 (p) outliers start: 17 outliers final: 13 residues processed: 161 average time/residue: 0.1129 time to fit residues: 27.4770 Evaluate side-chains 152 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 202 HIS Chi-restraints excluded: chain I residue 46 TYR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 861 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 149 GLN F 231 HIS ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093124 restraints weight = 21367.915| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.45 r_work: 0.2968 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15685 Z= 0.174 Angle : 0.554 6.772 21232 Z= 0.292 Chirality : 0.045 0.150 2266 Planarity : 0.004 0.035 2725 Dihedral : 5.812 55.166 2152 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.89 % Favored : 91.96 % Rotamer: Outliers : 1.15 % Allowed : 9.84 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -1.27 (0.19), residues: 1902 helix: -0.40 (0.45), residues: 135 sheet: 0.13 (0.19), residues: 800 loop : -1.80 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 119 TYR 0.023 0.001 TYR G 220 PHE 0.017 0.002 PHE G 92 TRP 0.007 0.001 TRP H 227 HIS 0.004 0.001 HIS F 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 (15683) covalent geometry : angle 0.55432 / 0.29 (21232) hydrogen bonds : bond 0.03184 / 2.01 ( 450) hydrogen bonds : angle 5.00106 / 3.30 ( 1170) Misc. bond : bond 0.00034 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.488 Fit side-chains REVERT: F 179 PHE cc_start: 0.5786 (t80) cc_final: 0.5455 (m-10) REVERT: F 280 MET cc_start: 0.8117 (mpp) cc_final: 0.7823 (mmm) REVERT: G 98 ASP cc_start: 0.8144 (t0) cc_final: 0.7916 (t70) REVERT: H 127 MET cc_start: 0.7967 (ttt) cc_final: 0.7469 (tpt) REVERT: H 334 ILE cc_start: 0.8555 (pt) cc_final: 0.8284 (pt) REVERT: H 424 ASP cc_start: 0.7593 (t70) cc_final: 0.7052 (t0) REVERT: H 446 TRP cc_start: 0.9070 (m100) cc_final: 0.8412 (m100) REVERT: J 56 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6866 (tp30) REVERT: J 186 TYR cc_start: 0.8036 (t80) cc_final: 0.7655 (t80) REVERT: A 705 SER cc_start: 0.7528 (t) cc_final: 0.7191 (p) outliers start: 19 outliers final: 16 residues processed: 160 average time/residue: 0.1177 time to fit residues: 28.9271 Evaluate side-chains 155 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 19 CYS Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 202 HIS Chi-restraints excluded: chain I residue 46 TYR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 861 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 140 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 149 GLN ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 381 HIS G 385 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.094674 restraints weight = 21305.458| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.45 r_work: 0.2991 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15685 Z= 0.123 Angle : 0.512 6.715 21232 Z= 0.271 Chirality : 0.044 0.142 2266 Planarity : 0.003 0.036 2725 Dihedral : 5.601 56.266 2152 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.62 % Favored : 93.22 % Rotamer: Outliers : 1.57 % Allowed : 10.44 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -1.24 (0.19), residues: 1902 helix: -0.35 (0.45), residues: 135 sheet: 0.14 (0.19), residues: 802 loop : -1.78 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.015 0.001 TYR G 220 PHE 0.012 0.001 PHE G 92 TRP 0.006 0.001 TRP I 144 HIS 0.007 0.001 HIS F 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (15683) covalent geometry : angle 0.51186 / 0.27 (21232) hydrogen bonds : bond 0.02831 / 1.80 ( 450) hydrogen bonds : angle 4.88902 / 3.22 ( 1170) Misc. bond : bond 0.00005 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.628 Fit side-chains REVERT: G 98 ASP cc_start: 0.8102 (t0) cc_final: 0.7710 (t70) REVERT: G 147 ASP cc_start: 0.7657 (m-30) cc_final: 0.7402 (m-30) REVERT: H 99 ARG cc_start: 0.6530 (mmm-85) cc_final: 0.6143 (mmm-85) REVERT: H 127 MET cc_start: 0.7905 (ttt) cc_final: 0.7390 (tpt) REVERT: H 334 ILE cc_start: 0.8518 (pt) cc_final: 0.8253 (pt) REVERT: H 424 ASP cc_start: 0.7558 (t70) cc_final: 0.6989 (t0) REVERT: H 446 TRP cc_start: 0.9023 (m100) cc_final: 0.8360 (m100) REVERT: J 56 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6918 (tp30) REVERT: J 141 GLU cc_start: 0.7866 (tp30) cc_final: 0.7662 (tp30) REVERT: J 186 TYR cc_start: 0.7954 (t80) cc_final: 0.7493 (t80) REVERT: A 705 SER cc_start: 0.7538 (t) cc_final: 0.7223 (p) outliers start: 26 outliers final: 17 residues processed: 165 average time/residue: 0.1156 time to fit residues: 29.4778 Evaluate side-chains 159 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 19 CYS Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 426 PHE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 202 HIS Chi-restraints excluded: chain I residue 46 TYR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 861 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 29 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 32 optimal weight: 0.1980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 149 GLN ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 381 HIS G 385 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.134883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.091758 restraints weight = 21335.048| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.44 r_work: 0.2954 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15685 Z= 0.195 Angle : 0.567 6.858 21232 Z= 0.299 Chirality : 0.045 0.152 2266 Planarity : 0.004 0.036 2725 Dihedral : 5.775 51.439 2152 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.20 % Favored : 91.64 % Rotamer: Outliers : 1.69 % Allowed : 10.92 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -1.38 (0.19), residues: 1902 helix: -0.40 (0.45), residues: 133 sheet: 0.06 (0.19), residues: 795 loop : -1.88 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.023 0.001 TYR G 220 PHE 0.018 0.002 PHE G 92 TRP 0.006 0.001 TRP H 227 HIS 0.007 0.001 HIS F 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.19 (15683) covalent geometry : angle 0.56740 / 0.30 (21232) hydrogen bonds : bond 0.03207 / 2.02 ( 450) hydrogen bonds : angle 5.01962 / 3.30 ( 1170) Misc. bond : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.649 Fit side-chains REVERT: G 98 ASP cc_start: 0.8161 (t0) cc_final: 0.7781 (t70) REVERT: H 99 ARG cc_start: 0.6537 (mmm-85) cc_final: 0.6216 (mmm-85) REVERT: H 127 MET cc_start: 0.8011 (ttt) cc_final: 0.7549 (tpt) REVERT: H 334 ILE cc_start: 0.8576 (pt) cc_final: 0.8283 (pt) REVERT: H 424 ASP cc_start: 0.7612 (t70) cc_final: 0.7064 (t0) REVERT: H 446 TRP cc_start: 0.9093 (m100) cc_final: 0.8439 (m100) REVERT: J 56 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7065 (tp30) REVERT: J 141 GLU cc_start: 0.7905 (tp30) cc_final: 0.7701 (tp30) REVERT: J 186 TYR cc_start: 0.7966 (t80) cc_final: 0.7469 (t80) REVERT: A 705 SER cc_start: 0.7600 (t) cc_final: 0.7283 (p) outliers start: 28 outliers final: 20 residues processed: 167 average time/residue: 0.1157 time to fit residues: 29.9163 Evaluate side-chains 163 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain G residue 19 CYS Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 426 PHE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 202 HIS Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain I residue 46 TYR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain A residue 768 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 163 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 381 HIS G 385 ASN I 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092113 restraints weight = 21189.274| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.44 r_work: 0.2963 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15685 Z= 0.175 Angle : 0.553 9.579 21232 Z= 0.291 Chirality : 0.045 0.177 2266 Planarity : 0.004 0.036 2725 Dihedral : 5.766 55.147 2152 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.73 % Favored : 92.17 % Rotamer: Outliers : 1.51 % Allowed : 11.89 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -1.39 (0.19), residues: 1902 helix: -0.42 (0.45), residues: 133 sheet: 0.05 (0.19), residues: 792 loop : -1.88 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.021 0.001 TYR G 220 PHE 0.016 0.001 PHE G 92 TRP 0.006 0.001 TRP A 716 HIS 0.006 0.001 HIS F 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.17 (15683) covalent geometry : angle 0.55306 / 0.29 (21232) hydrogen bonds : bond 0.03040 / 1.92 ( 450) hydrogen bonds : angle 4.96778 / 3.27 ( 1170) Misc. bond : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.633 Fit side-chains REVERT: G 98 ASP cc_start: 0.8198 (t0) cc_final: 0.7832 (t70) REVERT: G 230 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7352 (t80) REVERT: H 99 ARG cc_start: 0.6591 (mmm-85) cc_final: 0.6219 (mmm-85) REVERT: H 127 MET cc_start: 0.8011 (ttt) cc_final: 0.7517 (tpt) REVERT: H 334 ILE cc_start: 0.8556 (pt) cc_final: 0.8251 (pt) REVERT: H 424 ASP cc_start: 0.7475 (t70) cc_final: 0.6928 (t0) REVERT: H 446 TRP cc_start: 0.9023 (m100) cc_final: 0.8310 (m100) REVERT: J 56 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7065 (tp30) REVERT: J 141 GLU cc_start: 0.7882 (tp30) cc_final: 0.7664 (tp30) REVERT: J 186 TYR cc_start: 0.7999 (t80) cc_final: 0.7463 (t80) REVERT: A 705 SER cc_start: 0.7605 (t) cc_final: 0.7297 (p) REVERT: A 857 MET cc_start: 0.4907 (mtt) cc_final: 0.4648 (tpp) outliers start: 25 outliers final: 22 residues processed: 170 average time/residue: 0.1274 time to fit residues: 32.7765 Evaluate side-chains 168 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 19 CYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 426 PHE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 202 HIS Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain I residue 46 TYR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 861 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 130 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 388 ASN G 381 HIS G 385 ASN I 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092855 restraints weight = 21293.302| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.44 r_work: 0.2974 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15685 Z= 0.139 Angle : 0.534 11.156 21232 Z= 0.281 Chirality : 0.044 0.220 2266 Planarity : 0.004 0.067 2725 Dihedral : 5.632 49.872 2152 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.57 % Favored : 92.32 % Rotamer: Outliers : 1.51 % Allowed : 12.37 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -1.33 (0.19), residues: 1902 helix: -0.31 (0.45), residues: 131 sheet: 0.09 (0.19), residues: 792 loop : -1.85 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.017 0.001 TYR G 220 PHE 0.013 0.001 PHE G 92 TRP 0.005 0.001 TRP A 716 HIS 0.005 0.001 HIS F 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (15683) covalent geometry : angle 0.53353 / 0.28 (21232) hydrogen bonds : bond 0.02856 / 1.81 ( 450) hydrogen bonds : angle 4.88921 / 3.22 ( 1170) Misc. bond : bond 0.00007 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.612 Fit side-chains REVERT: G 98 ASP cc_start: 0.8161 (t0) cc_final: 0.7805 (t70) REVERT: G 230 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7328 (t80) REVERT: H 99 ARG cc_start: 0.6656 (mmm-85) cc_final: 0.6283 (mmm-85) REVERT: H 127 MET cc_start: 0.8024 (ttt) cc_final: 0.7540 (tpt) REVERT: H 334 ILE cc_start: 0.8555 (pt) cc_final: 0.8245 (pt) REVERT: H 403 MET cc_start: 0.8602 (mmm) cc_final: 0.8329 (mmm) REVERT: H 424 ASP cc_start: 0.7532 (t70) cc_final: 0.7009 (t0) REVERT: H 446 TRP cc_start: 0.9049 (m100) cc_final: 0.8454 (m100) REVERT: J 56 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7086 (tp30) REVERT: J 141 GLU cc_start: 0.7889 (tp30) cc_final: 0.7676 (tp30) REVERT: J 186 TYR cc_start: 0.7975 (t80) cc_final: 0.7434 (t80) REVERT: A 606 MET cc_start: 0.7983 (mtm) cc_final: 0.7333 (mtt) REVERT: A 705 SER cc_start: 0.7646 (t) cc_final: 0.7345 (p) REVERT: A 857 MET cc_start: 0.4877 (mtt) cc_final: 0.4627 (tpp) outliers start: 25 outliers final: 22 residues processed: 163 average time/residue: 0.1165 time to fit residues: 29.3696 Evaluate side-chains 165 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 19 CYS Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 426 PHE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 202 HIS Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain I residue 46 TYR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 861 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 148 optimal weight: 0.2980 chunk 179 optimal weight: 0.5980 chunk 165 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN G 186 ASN G 381 HIS G 385 ASN G 424 ASN H 266 HIS I 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.095526 restraints weight = 21142.990| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.44 r_work: 0.3007 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15685 Z= 0.098 Angle : 0.504 12.392 21232 Z= 0.264 Chirality : 0.043 0.210 2266 Planarity : 0.003 0.060 2725 Dihedral : 5.376 48.962 2152 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.22 % Rotamer: Outliers : 1.51 % Allowed : 12.43 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -1.23 (0.19), residues: 1902 helix: -0.34 (0.44), residues: 138 sheet: 0.14 (0.19), residues: 808 loop : -1.78 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.014 0.001 TYR A 713 PHE 0.029 0.001 PHE A 648 TRP 0.009 0.001 TRP H 117 HIS 0.004 0.001 HIS F 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (15683) covalent geometry : angle 0.50395 / 0.26 (21232) hydrogen bonds : bond 0.02517 / 1.62 ( 450) hydrogen bonds : angle 4.71927 / 3.11 ( 1170) Misc. bond : bond 0.00012 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.617 Fit side-chains REVERT: G 98 ASP cc_start: 0.8097 (t0) cc_final: 0.7744 (t70) REVERT: G 147 ASP cc_start: 0.7616 (m-30) cc_final: 0.7342 (m-30) REVERT: H 99 ARG cc_start: 0.6729 (mmm-85) cc_final: 0.6344 (mmm-85) REVERT: H 119 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7858 (mmm-85) REVERT: H 127 MET cc_start: 0.7914 (ttt) cc_final: 0.7458 (tpt) REVERT: H 225 ARG cc_start: 0.8774 (ttm170) cc_final: 0.8451 (tpp80) REVERT: H 403 MET cc_start: 0.8570 (mmm) cc_final: 0.8290 (mmm) REVERT: H 446 TRP cc_start: 0.8936 (m100) cc_final: 0.8313 (m100) REVERT: I 52 PHE cc_start: 0.7494 (m-80) cc_final: 0.7253 (m-80) REVERT: J 186 TYR cc_start: 0.7909 (t80) cc_final: 0.7327 (t80) REVERT: A 606 MET cc_start: 0.7916 (mtm) cc_final: 0.7245 (mtt) REVERT: A 857 MET cc_start: 0.4888 (mtt) cc_final: 0.4662 (tpp) outliers start: 25 outliers final: 20 residues processed: 177 average time/residue: 0.1235 time to fit residues: 33.3151 Evaluate side-chains 168 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 426 PHE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 202 HIS Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain I residue 46 TYR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 861 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 chunk 131 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 chunk 107 optimal weight: 0.0670 chunk 145 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095630 restraints weight = 21215.487| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.48 r_work: 0.3008 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15685 Z= 0.099 Angle : 0.514 14.202 21232 Z= 0.268 Chirality : 0.043 0.221 2266 Planarity : 0.003 0.063 2725 Dihedral : 5.309 48.289 2152 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.62 % Favored : 93.27 % Rotamer: Outliers : 1.33 % Allowed : 13.28 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -1.16 (0.19), residues: 1902 helix: -0.28 (0.44), residues: 138 sheet: 0.19 (0.19), residues: 810 loop : -1.74 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.015 0.001 TYR I 145 PHE 0.032 0.001 PHE A 648 TRP 0.008 0.001 TRP H 117 HIS 0.005 0.001 HIS A 649 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (15683) covalent geometry : angle 0.51446 / 0.27 (21232) hydrogen bonds : bond 0.02491 / 1.59 ( 450) hydrogen bonds : angle 4.64212 / 3.06 ( 1170) Misc. bond : bond 0.00006 / 0.00 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.629 Fit side-chains REVERT: G 98 ASP cc_start: 0.8140 (t0) cc_final: 0.7777 (t70) REVERT: G 147 ASP cc_start: 0.7608 (m-30) cc_final: 0.7349 (m-30) REVERT: H 99 ARG cc_start: 0.6678 (mmm-85) cc_final: 0.6253 (mmm-85) REVERT: H 119 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7901 (mmm-85) REVERT: H 127 MET cc_start: 0.7925 (ttt) cc_final: 0.7440 (tpt) REVERT: H 225 ARG cc_start: 0.8756 (ttm170) cc_final: 0.8430 (tpp80) REVERT: H 403 MET cc_start: 0.8524 (mmm) cc_final: 0.8243 (mmm) REVERT: H 424 ASP cc_start: 0.7543 (t70) cc_final: 0.6989 (t0) REVERT: H 446 TRP cc_start: 0.8917 (m100) cc_final: 0.8266 (m100) REVERT: J 186 TYR cc_start: 0.7869 (t80) cc_final: 0.7280 (t80) REVERT: A 535 PHE cc_start: 0.6953 (t80) cc_final: 0.6346 (t80) REVERT: A 606 MET cc_start: 0.7878 (mtm) cc_final: 0.7229 (mtt) REVERT: A 857 MET cc_start: 0.4815 (mtt) cc_final: 0.4578 (tpp) outliers start: 22 outliers final: 22 residues processed: 167 average time/residue: 0.1196 time to fit residues: 30.4352 Evaluate side-chains 168 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 426 PHE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 202 HIS Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain I residue 46 TYR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 861 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 144 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 162 optimal weight: 0.0370 chunk 123 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN G 381 HIS G 385 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.094918 restraints weight = 21070.791| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.45 r_work: 0.3004 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15685 Z= 0.104 Angle : 0.516 13.224 21232 Z= 0.268 Chirality : 0.043 0.229 2266 Planarity : 0.003 0.063 2725 Dihedral : 5.305 47.795 2152 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.73 % Favored : 93.17 % Rotamer: Outliers : 1.33 % Allowed : 13.40 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -1.13 (0.19), residues: 1902 helix: -0.27 (0.44), residues: 140 sheet: 0.25 (0.19), residues: 801 loop : -1.75 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.015 0.001 TYR I 145 PHE 0.029 0.001 PHE A 645 TRP 0.007 0.001 TRP H 117 HIS 0.004 0.001 HIS F 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (15683) covalent geometry : angle 0.51612 / 0.27 (21232) hydrogen bonds : bond 0.02505 / 1.60 ( 450) hydrogen bonds : angle 4.61976 / 3.05 ( 1170) Misc. bond : bond 0.00004 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4056.58 seconds wall clock time: 70 minutes 16.43 seconds (4216.43 seconds total)