Starting phenix.real_space_refine on Wed Feb 4 17:43:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5t_45224/02_2026/9c5t_45224.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5t_45224/02_2026/9c5t_45224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c5t_45224/02_2026/9c5t_45224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5t_45224/02_2026/9c5t_45224.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c5t_45224/02_2026/9c5t_45224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5t_45224/02_2026/9c5t_45224.map" } resolution = 3.36 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= 0.034 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 64 5.16 5 C 7463 2.51 5 N 1990 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11781 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3036 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 16, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 8745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8745 Classifications: {'peptide': 1117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1076} Chain breaks: 4 Time building chain proxies: 2.82, per 1000 atoms: 0.24 Number of scatterers: 11781 At special positions: 0 Unit cell: (101.748, 101.748, 142.614, 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 64 16.00 O 2264 8.00 N 1990 7.00 C 7463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 379 " distance=2.06 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 313 " distance=2.05 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: 0.90 Conformation dependent library (CDL) restraints added in 553.2 milliseconds 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2792 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 32 sheets defined 5.4% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Proline residue: A 10 - end of helix Processing helix chain 'A' and resid 27 through 30 removed outlier: 4.199A pdb=" N THR A 30 " --> pdb=" O SER A 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 27 through 30' Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 1044 through 1062 Processing helix chain 'B' and resid 1069 through 1074 Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1101 through 1110 removed outlier: 3.555A pdb=" N GLU B1107 " --> pdb=" O PRO B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1138 removed outlier: 3.502A pdb=" N LEU B1129 " --> pdb=" O THR B1125 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B1138 " --> pdb=" O GLU B1134 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 323 through 325 removed outlier: 3.651A pdb=" N ALA A 341 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS A 34 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TRP A 408 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR A 32 " --> pdb=" O TRP A 408 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N SER A 35 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 387 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 70 removed outlier: 4.099A pdb=" N LYS A 92 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.346A pdb=" N ALA A 116 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU A 104 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 114 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TRP A 106 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS A 112 " --> pdb=" O TRP A 106 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 115 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 123 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 117 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 134 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASP A 126 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 132 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 149 removed outlier: 4.129A pdb=" N SER A 149 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 155 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 183 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP A 169 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLN A 181 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 224 removed outlier: 3.797A pdb=" N VAL A 221 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 279 removed outlier: 3.979A pdb=" N SER A 276 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 309 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1041 through 1042 removed outlier: 6.587A pdb=" N ASN B 4 " --> pdb=" O ILE B1089 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.373A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B1006 " --> pdb=" O GLY B1031 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 19 through 21 removed outlier: 6.041A pdb=" N VAL B 43 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 67 removed outlier: 3.707A pdb=" N THR B 81 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 104 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU B 90 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR B 102 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS B 92 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE B 100 " --> pdb=" O LYS B 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 121 through 124 removed outlier: 3.894A pdb=" N ILE B 121 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 163 through 169 removed outlier: 4.510A pdb=" N HIS B 163 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 218 through 221 removed outlier: 3.700A pdb=" N MET B 218 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 232 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 246 " --> pdb=" O TYR B 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 261 through 263 removed outlier: 7.449A pdb=" N LEU B 280 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU B 304 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N MET B 282 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL B 302 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 284 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU B 300 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU B 286 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.441A pdb=" N GLY B 325 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B 314 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE B 323 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TYR B 316 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 321 " --> pdb=" O TYR B 316 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 362 through 365 Processing sheet with id=AB8, first strand: chain 'B' and resid 412 through 413 removed outlier: 3.559A pdb=" N THR B 424 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 462 through 464 removed outlier: 3.993A pdb=" N ALA B 464 " --> pdb=" O GLN B 467 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 500 through 504 Processing sheet with id=AC2, first strand: chain 'B' and resid 515 through 516 Processing sheet with id=AC3, first strand: chain 'B' and resid 557 through 558 removed outlier: 3.726A pdb=" N ILE B 558 " --> pdb=" O ARG B 567 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 588 through 595 Processing sheet with id=AC5, first strand: chain 'B' and resid 611 through 612 Processing sheet with id=AC6, first strand: chain 'B' and resid 640 through 641 Processing sheet with id=AC7, first strand: chain 'B' and resid 678 through 680 removed outlier: 4.067A pdb=" N TYR B 678 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 726 through 727 Processing sheet with id=AC9, first strand: chain 'B' and resid 749 through 751 removed outlier: 7.465A pdb=" N HIS B 789 " --> pdb=" O GLN B 806 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN B 806 " --> pdb=" O HIS B 789 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU B 791 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 804 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 793 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER B 764 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 811 through 819 removed outlier: 6.696A pdb=" N GLY B 832 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 816 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B 830 " --> pdb=" O LEU B 816 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER B 818 " --> pdb=" O TYR B 828 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR B 828 " --> pdb=" O SER B 818 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN B 845 " --> pdb=" O MET B 835 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 870 through 876 removed outlier: 4.366A pdb=" N SER B 872 " --> pdb=" O SER B 883 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 874 " --> pdb=" O LEU B 881 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 881 " --> pdb=" O VAL B 874 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 913 through 917 removed outlier: 6.722A pdb=" N ALA B 934 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU B 944 " --> pdb=" O ALA B 934 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 954 through 959 removed outlier: 6.904A pdb=" N ALA B 968 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL B 957 " --> pdb=" O LEU B 966 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B 966 " --> pdb=" O VAL B 957 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 975 " --> pdb=" O GLY B 967 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 973 " --> pdb=" O GLU B 969 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1076 through 1077 283 hydrogen bonds defined for protein. 723 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: 2.53 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3882 1.34 - 1.46: 2353 1.46 - 1.58: 5684 1.58 - 1.69: 1 1.69 - 1.81: 95 Bond restraints: 12015 Sorted by residual: bond pdb=" CA ASP B 366 " pdb=" CB ASP B 366 " ideal model delta sigma weight residual 1.530 1.577 -0.047 1.50e-02 4.44e+03 9.77e+00 bond pdb=" CA VAL B 512 " pdb=" CB VAL B 512 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.17e+00 bond pdb=" CB GLU B 215 " pdb=" CG GLU B 215 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.83e-01 bond pdb=" CA SER B 762 " pdb=" C SER B 762 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.74e-01 bond pdb=" CB GLN B 174 " pdb=" CG GLN B 174 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.38e-01 ... (remaining 12010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 15950 1.48 - 2.96: 267 2.96 - 4.44: 49 4.44 - 5.92: 11 5.92 - 7.40: 4 Bond angle restraints: 16281 Sorted by residual: angle pdb=" C ASP A 401 " pdb=" CA ASP A 401 " pdb=" CB ASP A 401 " ideal model delta sigma weight residual 115.79 110.56 5.23 1.19e+00 7.06e-01 1.93e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 121.80 -7.40 2.30e+00 1.89e-01 1.03e+01 angle pdb=" N VAL B 995 " pdb=" CA VAL B 995 " pdb=" C VAL B 995 " ideal model delta sigma weight residual 111.62 109.15 2.47 7.90e-01 1.60e+00 9.81e+00 angle pdb=" CA GLU B 215 " pdb=" CB GLU B 215 " pdb=" CG GLU B 215 " ideal model delta sigma weight residual 114.10 120.27 -6.17 2.00e+00 2.50e-01 9.51e+00 angle pdb=" C ASP B 366 " pdb=" CA ASP B 366 " pdb=" CB ASP B 366 " ideal model delta sigma weight residual 110.16 115.05 -4.89 1.66e+00 3.63e-01 8.68e+00 ... (remaining 16276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6117 17.69 - 35.37: 807 35.37 - 53.06: 192 53.06 - 70.75: 62 70.75 - 88.43: 20 Dihedral angle restraints: 7198 sinusoidal: 2861 harmonic: 4337 Sorted by residual: dihedral pdb=" CB CYS A 55 " pdb=" SG CYS A 55 " pdb=" SG CYS A 379 " pdb=" CB CYS A 379 " ideal model delta sinusoidal sigma weight residual 93.00 166.16 -73.16 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CA ALA B 692 " pdb=" C ALA B 692 " pdb=" N LEU B 693 " pdb=" CA LEU B 693 " ideal model delta harmonic sigma weight residual -180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA CYS A 379 " pdb=" C CYS A 379 " pdb=" N SER A 380 " pdb=" CA SER A 380 " ideal model delta harmonic sigma weight residual 180.00 -162.97 -17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 7195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1076 0.027 - 0.055: 462 0.055 - 0.082: 139 0.082 - 0.110: 117 0.110 - 0.137: 55 Chirality restraints: 1849 Sorted by residual: chirality pdb=" CA ARG A 253 " pdb=" N ARG A 253 " pdb=" C ARG A 253 " pdb=" CB ARG A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE B 591 " pdb=" N ILE B 591 " pdb=" C ILE B 591 " pdb=" CB ILE B 591 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA VAL A 107 " pdb=" N VAL A 107 " pdb=" C VAL A 107 " pdb=" CB VAL A 107 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1846 not shown) Planarity restraints: 2097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 906 " -0.017 2.00e-02 2.50e+03 1.49e-02 4.47e+00 pdb=" CG TYR B 906 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 906 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 906 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 906 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 906 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 906 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 906 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 222 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO B 223 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 223 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 223 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 366 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C ASP B 366 " 0.028 2.00e-02 2.50e+03 pdb=" O ASP B 366 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 367 " -0.009 2.00e-02 2.50e+03 ... (remaining 2094 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 370 2.70 - 3.25: 11234 3.25 - 3.80: 18482 3.80 - 4.35: 23671 4.35 - 4.90: 41248 Nonbonded interactions: 95005 Sorted by model distance: nonbonded pdb=" O THR A 250 " pdb=" NH2 ARG A 253 " model vdw 2.150 3.120 nonbonded pdb=" OG SER B 256 " pdb=" OD1 ASP B 275 " model vdw 2.170 3.040 nonbonded pdb=" OD1 ASN A 248 " pdb=" OG1 THR A 250 " model vdw 2.195 3.040 nonbonded pdb=" OG SER B 886 " pdb=" O ASN B 908 " model vdw 2.217 3.040 nonbonded pdb=" OG SER B 480 " pdb=" O ALA B 485 " model vdw 2.219 3.040 ... (remaining 95000 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: 1.880 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: 0.040 Process input model: 12.730 Find NCS groups from input model: 0.050 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12017 Z= 0.116 Angle : 0.518 7.479 16285 Z= 0.277 Chirality : 0.043 0.137 1849 Planarity : 0.003 0.051 2097 Dihedral : 17.768 88.431 4400 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.44 % Rotamer: Outliers : 0.38 % Allowed : 25.25 % Favored : 74.37 % 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: -2.28 (0.21), residues: 1492 helix: 0.63 (0.64), residues: 74 sheet: -1.84 (0.22), residues: 557 loop : -1.45 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.036 0.001 TYR B 906 PHE 0.012 0.001 PHE A 53 TRP 0.011 0.001 TRP B1073 HIS 0.006 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00249 (12015) covalent geometry : angle 0.51371 (16281) SS BOND : bond 0.02475 ( 2) SS BOND : angle 4.46930 ( 4) hydrogen bonds : bond 0.25568 ( 283) hydrogen bonds : angle 11.19703 ( 723) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: B 1014 MET cc_start: 0.5930 (ptm) cc_final: 0.5659 (ptp) outliers start: 5 outliers final: 2 residues processed: 104 average time/residue: 0.1086 time to fit residues: 16.9298 Evaluate side-chains 97 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 1011 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0570 chunk 55 optimal weight: 0.0870 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 ASN B 696 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.182549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.136343 restraints weight = 14464.614| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.97 r_work: 0.3165 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12017 Z= 0.096 Angle : 0.503 5.832 16285 Z= 0.263 Chirality : 0.044 0.151 1849 Planarity : 0.003 0.044 2097 Dihedral : 3.965 29.865 1608 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.38 % Rotamer: Outliers : 2.59 % Allowed : 22.89 % Favored : 74.52 % 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: -2.19 (0.21), residues: 1492 helix: 0.72 (0.64), residues: 74 sheet: -1.69 (0.21), residues: 554 loop : -1.45 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1057 TYR 0.017 0.001 TYR B 906 PHE 0.018 0.001 PHE B1030 TRP 0.013 0.001 TRP A 243 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00216 (12015) covalent geometry : angle 0.50245 (16281) SS BOND : bond 0.00402 ( 2) SS BOND : angle 2.03474 ( 4) hydrogen bonds : bond 0.03819 ( 283) hydrogen bonds : angle 7.21423 ( 723) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8580 (mp0) cc_final: 0.8211 (mp0) REVERT: B 892 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8093 (pt0) REVERT: B 896 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: B 910 MET cc_start: 0.8136 (mmm) cc_final: 0.7872 (ttm) REVERT: B 945 ILE cc_start: 0.9196 (mm) cc_final: 0.8966 (mt) outliers start: 34 outliers final: 11 residues processed: 136 average time/residue: 0.0860 time to fit residues: 17.9856 Evaluate side-chains 110 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 929 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 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 = 0.4092 r_free = 0.4092 target = 0.176656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128935 restraints weight = 14702.277| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.40 r_work: 0.3006 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12017 Z= 0.216 Angle : 0.575 6.418 16285 Z= 0.297 Chirality : 0.046 0.158 1849 Planarity : 0.004 0.047 2097 Dihedral : 4.285 36.095 1606 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 3.35 % Allowed : 24.11 % Favored : 72.55 % 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: -2.21 (0.21), residues: 1492 helix: 0.51 (0.63), residues: 74 sheet: -1.68 (0.21), residues: 551 loop : -1.47 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 388 TYR 0.018 0.002 TYR B 906 PHE 0.015 0.002 PHE B 998 TRP 0.011 0.001 TRP B 207 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00525 (12015) covalent geometry : angle 0.57396 (16281) SS BOND : bond 0.00286 ( 2) SS BOND : angle 2.18828 ( 4) hydrogen bonds : bond 0.04009 ( 283) hydrogen bonds : angle 6.92530 ( 723) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7191 (p0) REVERT: B 541 LEU cc_start: 0.1523 (OUTLIER) cc_final: 0.1095 (mp) REVERT: B 679 MET cc_start: 0.6127 (ppp) cc_final: 0.5022 (tmm) REVERT: B 892 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8074 (pt0) REVERT: B 896 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: B 910 MET cc_start: 0.8447 (mmm) cc_final: 0.8182 (ttm) REVERT: B 1014 MET cc_start: 0.6248 (ptm) cc_final: 0.6021 (ptp) outliers start: 44 outliers final: 28 residues processed: 135 average time/residue: 0.0946 time to fit residues: 19.8581 Evaluate side-chains 121 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 TRP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1062 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 120 optimal weight: 0.0570 chunk 86 optimal weight: 20.0000 chunk 142 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 0.0270 chunk 107 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 overall best weight: 1.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS B 105 HIS ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.177038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129035 restraints weight = 14627.466| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.45 r_work: 0.2963 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12017 Z= 0.183 Angle : 0.554 6.668 16285 Z= 0.285 Chirality : 0.045 0.157 1849 Planarity : 0.003 0.048 2097 Dihedral : 4.319 44.312 1606 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 4.11 % Allowed : 23.88 % Favored : 72.02 % 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: -2.17 (0.21), residues: 1492 helix: 0.54 (0.64), residues: 74 sheet: -1.57 (0.21), residues: 534 loop : -1.52 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.012 0.001 TYR B 906 PHE 0.013 0.001 PHE B 998 TRP 0.012 0.001 TRP B 207 HIS 0.003 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00443 (12015) covalent geometry : angle 0.55078 (16281) SS BOND : bond 0.00796 ( 2) SS BOND : angle 3.72249 ( 4) hydrogen bonds : bond 0.03551 ( 283) hydrogen bonds : angle 6.56330 ( 723) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 96 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7169 (p0) REVERT: A 166 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7136 (mpp) REVERT: B 449 MET cc_start: 0.4875 (ppp) cc_final: 0.3404 (mmm) REVERT: B 541 LEU cc_start: 0.1526 (OUTLIER) cc_final: 0.1102 (mp) REVERT: B 679 MET cc_start: 0.6101 (ppp) cc_final: 0.5310 (mmt) REVERT: B 904 ASN cc_start: 0.7494 (t0) cc_final: 0.7257 (t0) REVERT: B 910 MET cc_start: 0.8366 (mmm) cc_final: 0.8126 (ttm) REVERT: B 1014 MET cc_start: 0.6296 (ptm) cc_final: 0.6063 (ptp) outliers start: 54 outliers final: 32 residues processed: 141 average time/residue: 0.1012 time to fit residues: 21.7822 Evaluate side-chains 129 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 TRP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1062 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 11 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 8 optimal weight: 0.0870 chunk 77 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 82 optimal weight: 0.0770 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 HIS ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 GLN B 531 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.180224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133034 restraints weight = 14591.082| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.18 r_work: 0.3055 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12017 Z= 0.101 Angle : 0.502 6.625 16285 Z= 0.257 Chirality : 0.044 0.174 1849 Planarity : 0.003 0.044 2097 Dihedral : 4.088 40.616 1606 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 3.12 % Allowed : 24.87 % Favored : 72.02 % 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: -2.06 (0.21), residues: 1492 helix: 0.78 (0.65), residues: 74 sheet: -1.45 (0.21), residues: 545 loop : -1.49 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.012 0.001 TYR B 42 PHE 0.012 0.001 PHE B1030 TRP 0.012 0.001 TRP B 207 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00240 (12015) covalent geometry : angle 0.50005 (16281) SS BOND : bond 0.00348 ( 2) SS BOND : angle 3.01289 ( 4) hydrogen bonds : bond 0.03016 ( 283) hydrogen bonds : angle 6.13883 ( 723) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8687 (mp0) cc_final: 0.8400 (mp0) REVERT: A 91 PHE cc_start: 0.8571 (p90) cc_final: 0.8287 (p90) REVERT: A 162 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7135 (p0) REVERT: A 166 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7219 (mpp) REVERT: B 149 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8075 (t0) REVERT: B 449 MET cc_start: 0.4849 (ppp) cc_final: 0.3465 (mmm) REVERT: B 528 GLN cc_start: 0.1740 (OUTLIER) cc_final: 0.0619 (mt0) REVERT: B 541 LEU cc_start: 0.1430 (OUTLIER) cc_final: 0.1016 (mp) REVERT: B 679 MET cc_start: 0.5923 (ppp) cc_final: 0.5228 (mmt) REVERT: B 892 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8012 (pt0) outliers start: 41 outliers final: 26 residues processed: 137 average time/residue: 0.1017 time to fit residues: 21.2056 Evaluate side-chains 128 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 168 TRP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 782 PHE Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1062 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 78 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.176489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127663 restraints weight = 14689.510| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.51 r_work: 0.3020 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12017 Z= 0.199 Angle : 0.570 7.192 16285 Z= 0.292 Chirality : 0.046 0.184 1849 Planarity : 0.003 0.049 2097 Dihedral : 4.337 42.213 1606 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 3.50 % Allowed : 24.94 % Favored : 71.56 % 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: -2.12 (0.21), residues: 1492 helix: 0.67 (0.64), residues: 74 sheet: -1.51 (0.21), residues: 551 loop : -1.50 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 388 TYR 0.016 0.001 TYR B 906 PHE 0.014 0.001 PHE B 998 TRP 0.010 0.001 TRP B 207 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00487 (12015) covalent geometry : angle 0.56658 (16281) SS BOND : bond 0.00982 ( 2) SS BOND : angle 4.19353 ( 4) hydrogen bonds : bond 0.03480 ( 283) hydrogen bonds : angle 6.29952 ( 723) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 96 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6917 (tp40) REVERT: A 162 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7091 (p0) REVERT: B 3 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: B 449 MET cc_start: 0.4874 (ppp) cc_final: 0.3658 (mmm) REVERT: B 541 LEU cc_start: 0.1391 (OUTLIER) cc_final: 0.0961 (mp) REVERT: B 892 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: B 1014 MET cc_start: 0.6289 (ptm) cc_final: 0.6072 (ptp) outliers start: 46 outliers final: 34 residues processed: 133 average time/residue: 0.0899 time to fit residues: 18.1078 Evaluate side-chains 130 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain B residue 3 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1062 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 116 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 141 optimal weight: 0.7980 chunk 92 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 99 optimal weight: 0.0670 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.179882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131477 restraints weight = 14586.539| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.68 r_work: 0.3022 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12017 Z= 0.110 Angle : 0.518 10.011 16285 Z= 0.263 Chirality : 0.044 0.158 1849 Planarity : 0.003 0.046 2097 Dihedral : 4.064 39.810 1606 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 3.42 % Allowed : 25.32 % Favored : 71.25 % 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: -2.02 (0.21), residues: 1492 helix: 0.89 (0.65), residues: 74 sheet: -1.42 (0.21), residues: 540 loop : -1.48 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.012 0.001 TYR B 906 PHE 0.013 0.001 PHE B1030 TRP 0.012 0.001 TRP B 207 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00263 (12015) covalent geometry : angle 0.51515 (16281) SS BOND : bond 0.00953 ( 2) SS BOND : angle 3.70823 ( 4) hydrogen bonds : bond 0.02976 ( 283) hydrogen bonds : angle 5.97008 ( 723) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6916 (tp40) REVERT: A 73 GLU cc_start: 0.8682 (mp0) cc_final: 0.8359 (mp0) REVERT: A 91 PHE cc_start: 0.8565 (p90) cc_final: 0.8246 (p90) REVERT: A 162 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7017 (p0) REVERT: A 166 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7184 (mpp) REVERT: B 3 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: B 149 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8043 (t0) REVERT: B 449 MET cc_start: 0.4766 (ppp) cc_final: 0.3646 (mmm) REVERT: B 541 LEU cc_start: 0.1290 (OUTLIER) cc_final: 0.0915 (mp) REVERT: B 679 MET cc_start: 0.6308 (ppp) cc_final: 0.5013 (mmt) REVERT: B 892 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7982 (pt0) outliers start: 45 outliers final: 29 residues processed: 132 average time/residue: 0.0973 time to fit residues: 19.8940 Evaluate side-chains 129 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain B residue 3 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 782 PHE Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 1013 VAL Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1046 SER Chi-restraints excluded: chain B residue 1062 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 40.0000 chunk 117 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 146 optimal weight: 0.0030 chunk 11 optimal weight: 7.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.175959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126973 restraints weight = 14643.698| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.46 r_work: 0.2977 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12017 Z= 0.222 Angle : 0.606 9.095 16285 Z= 0.308 Chirality : 0.046 0.158 1849 Planarity : 0.004 0.049 2097 Dihedral : 4.427 43.526 1606 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 3.65 % Allowed : 25.10 % Favored : 71.25 % 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: -2.16 (0.21), residues: 1492 helix: 0.13 (0.62), residues: 81 sheet: -1.46 (0.21), residues: 543 loop : -1.56 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.019 0.001 TYR B 613 PHE 0.016 0.002 PHE B 998 TRP 0.012 0.001 TRP A 168 HIS 0.004 0.001 HIS B1140 Details of bonding type rmsd covalent geometry : bond 0.00542 (12015) covalent geometry : angle 0.60228 (16281) SS BOND : bond 0.01034 ( 2) SS BOND : angle 4.16577 ( 4) hydrogen bonds : bond 0.03493 ( 283) hydrogen bonds : angle 6.27632 ( 723) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 94 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.6946 (tp40) REVERT: A 73 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: A 162 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7138 (p0) REVERT: A 180 ARG cc_start: 0.7232 (mmp-170) cc_final: 0.6601 (ptm-80) REVERT: B 3 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8624 (m-80) REVERT: B 318 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: B 449 MET cc_start: 0.4696 (ppp) cc_final: 0.3635 (mmm) REVERT: B 541 LEU cc_start: 0.1269 (OUTLIER) cc_final: 0.0801 (mp) REVERT: B 593 MET cc_start: 0.5956 (mtm) cc_final: 0.5726 (ttm) REVERT: B 679 MET cc_start: 0.6189 (ppp) cc_final: 0.4891 (mmt) REVERT: B 892 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: B 939 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: B 1014 MET cc_start: 0.6267 (ptm) cc_final: 0.6028 (ptp) outliers start: 48 outliers final: 35 residues processed: 130 average time/residue: 0.0953 time to fit residues: 18.9200 Evaluate side-chains 133 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain B residue 3 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 903 CYS Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1046 SER Chi-restraints excluded: chain B residue 1062 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 100 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.177705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.130169 restraints weight = 14431.259| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.12 r_work: 0.3170 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12017 Z= 0.152 Angle : 0.563 8.726 16285 Z= 0.284 Chirality : 0.045 0.159 1849 Planarity : 0.003 0.047 2097 Dihedral : 4.276 43.587 1606 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.44 % Rotamer: Outliers : 3.57 % Allowed : 25.10 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.11 (0.21), residues: 1492 helix: 0.27 (0.63), residues: 81 sheet: -1.40 (0.21), residues: 549 loop : -1.56 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.014 0.001 TYR B 906 PHE 0.013 0.001 PHE B 998 TRP 0.012 0.001 TRP B 207 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00371 (12015) covalent geometry : angle 0.55937 (16281) SS BOND : bond 0.00754 ( 2) SS BOND : angle 4.18483 ( 4) hydrogen bonds : bond 0.03134 ( 283) hydrogen bonds : angle 6.08064 ( 723) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6933 (tp40) REVERT: A 26 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: A 73 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: A 162 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7084 (p0) REVERT: A 166 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7567 (mpp) REVERT: A 180 ARG cc_start: 0.7207 (mmp-170) cc_final: 0.6734 (ptm-80) REVERT: B 3 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: B 149 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8113 (t0) REVERT: B 318 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: B 449 MET cc_start: 0.4788 (ppp) cc_final: 0.3796 (mmm) REVERT: B 541 LEU cc_start: 0.1264 (OUTLIER) cc_final: 0.0770 (mp) REVERT: B 593 MET cc_start: 0.5987 (mtm) cc_final: 0.5762 (ttm) REVERT: B 679 MET cc_start: 0.6269 (ppp) cc_final: 0.4981 (mmt) REVERT: B 892 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: B 939 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: B 1014 MET cc_start: 0.6401 (ptm) cc_final: 0.6167 (ptp) outliers start: 47 outliers final: 34 residues processed: 133 average time/residue: 0.0993 time to fit residues: 20.1903 Evaluate side-chains 140 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 3 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1046 SER Chi-restraints excluded: chain B residue 1062 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 67 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.178918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130718 restraints weight = 14573.531| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.62 r_work: 0.3031 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12017 Z= 0.130 Angle : 0.546 8.644 16285 Z= 0.275 Chirality : 0.044 0.148 1849 Planarity : 0.003 0.048 2097 Dihedral : 4.123 40.140 1606 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.16 % Favored : 94.77 % Rotamer: Outliers : 3.50 % Allowed : 25.63 % Favored : 70.87 % 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: -2.04 (0.21), residues: 1492 helix: 0.33 (0.63), residues: 81 sheet: -1.31 (0.21), residues: 545 loop : -1.55 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.013 0.001 TYR B 906 PHE 0.013 0.001 PHE B1030 TRP 0.012 0.001 TRP B 207 HIS 0.003 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00318 (12015) covalent geometry : angle 0.54222 (16281) SS BOND : bond 0.00679 ( 2) SS BOND : angle 4.11654 ( 4) hydrogen bonds : bond 0.02974 ( 283) hydrogen bonds : angle 5.93512 ( 723) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6910 (tp40) REVERT: A 73 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: A 91 PHE cc_start: 0.8574 (p90) cc_final: 0.8271 (p90) REVERT: A 162 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7057 (p0) REVERT: A 166 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7254 (mpp) REVERT: A 180 ARG cc_start: 0.7222 (mmp-170) cc_final: 0.6710 (ptm-80) REVERT: B 3 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8477 (m-80) REVERT: B 54 GLU cc_start: 0.8358 (tt0) cc_final: 0.8155 (tp30) REVERT: B 149 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8077 (t0) REVERT: B 215 GLU cc_start: 0.8198 (tp30) cc_final: 0.7967 (tp30) REVERT: B 318 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: B 449 MET cc_start: 0.4811 (ppp) cc_final: 0.3774 (mmm) REVERT: B 541 LEU cc_start: 0.1182 (OUTLIER) cc_final: 0.0718 (mp) REVERT: B 581 MET cc_start: 0.2067 (OUTLIER) cc_final: 0.1748 (tmm) REVERT: B 679 MET cc_start: 0.6211 (ppp) cc_final: 0.4963 (mmt) REVERT: B 892 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: B 939 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: B 1080 ARG cc_start: 0.8293 (mtp85) cc_final: 0.8015 (mtm110) outliers start: 46 outliers final: 33 residues processed: 139 average time/residue: 0.1054 time to fit residues: 21.5957 Evaluate side-chains 145 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 3 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1046 SER Chi-restraints excluded: chain B residue 1062 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 0.0370 chunk 111 optimal weight: 4.9990 chunk 135 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.182063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.135506 restraints weight = 14400.323| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.17 r_work: 0.3204 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12017 Z= 0.098 Angle : 0.527 8.602 16285 Z= 0.264 Chirality : 0.044 0.142 1849 Planarity : 0.003 0.047 2097 Dihedral : 3.940 34.558 1606 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.69 % Favored : 95.24 % Rotamer: Outliers : 2.89 % Allowed : 25.93 % Favored : 71.18 % 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: -1.92 (0.21), residues: 1492 helix: 1.01 (0.66), residues: 74 sheet: -1.24 (0.21), residues: 559 loop : -1.50 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.013 0.001 TYR B 906 PHE 0.013 0.001 PHE B1030 TRP 0.012 0.001 TRP B1073 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00236 (12015) covalent geometry : angle 0.52344 (16281) SS BOND : bond 0.00540 ( 2) SS BOND : angle 3.94279 ( 4) hydrogen bonds : bond 0.02770 ( 283) hydrogen bonds : angle 5.73104 ( 723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3548.47 seconds wall clock time: 61 minutes 31.76 seconds (3691.76 seconds total)