Starting phenix.real_space_refine on Wed Feb 4 01:13:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ltw_63383/02_2026/9ltw_63383.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ltw_63383/02_2026/9ltw_63383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ltw_63383/02_2026/9ltw_63383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ltw_63383/02_2026/9ltw_63383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ltw_63383/02_2026/9ltw_63383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ltw_63383/02_2026/9ltw_63383.map" } resolution = 3.25 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= -0.001 sd= 0.027 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 37 5.16 5 C 5143 2.51 5 N 1417 2.21 5 O 1407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 8004 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2056 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 8, 'TRANS': 305} Chain breaks: 6 Unresolved non-hydrogen bonds: 544 Unresolved non-hydrogen angles: 699 Unresolved non-hydrogen dihedrals: 442 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 10, 'PHE:plan': 11, 'GLU:plan': 15, 'ASP:plan': 13, 'ASN:plan1': 10, 'ARG:plan': 7, 'TYR:plan': 6, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 336 Chain: "B" Number of atoms: 5610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5610 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 748} Chain breaks: 5 Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 383 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 45, 'ARG:plan': 7, 'ASP:plan': 23, 'GLN:plan1': 10, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 341 Chain: "F" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 338 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 61 Time building chain proxies: 1.63, per 1000 atoms: 0.20 Number of scatterers: 8004 At special positions: 0 Unit cell: (95.2, 108.8, 93.5, 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 37 16.00 O 1407 8.00 N 1417 7.00 C 5143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 256.2 milliseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 22 sheets defined 8.9% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 17 through 26 removed outlier: 3.524A pdb=" N ARG A 24 " --> pdb=" O HIS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.815A pdb=" N GLN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 384 Processing helix chain 'B' and resid 1044 through 1059 Processing helix chain 'B' and resid 1069 through 1074 Processing helix chain 'B' and resid 1090 through 1097 removed outlier: 3.818A pdb=" N ILE B1094 " --> pdb=" O ASP B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1101 through 1106 Processing helix chain 'B' and resid 1127 through 1130 Processing helix chain 'B' and resid 1131 through 1136 removed outlier: 3.785A pdb=" N GLU B1135 " --> pdb=" O LYS B1131 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B1136 " --> pdb=" O VAL B1132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1131 through 1136' Processing helix chain 'F' and resid 55 through 60 removed outlier: 4.049A pdb=" N LEU F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.847A pdb=" N ASP F 64 " --> pdb=" O GLN F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65 removed outlier: 6.781A pdb=" N ILE A 73 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A 65 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR A 71 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 84 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 147 removed outlier: 4.428A pdb=" N ASN A 141 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLY A 157 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N GLU A 143 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N ILE A 155 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER A 158 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 192 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 195 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP A 205 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 228 through 229 removed outlier: 5.482A pdb=" N GLN A 243 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASP A 252 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 369 removed outlier: 7.151A pdb=" N VAL A 367 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 522 Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 10 removed outlier: 6.101A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B1030 " --> pdb=" O GLY B1038 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER B1042 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY B1026 " --> pdb=" O SER B1042 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N SER B1027 " --> pdb=" O HIS B1009 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N HIS B1009 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B1029 " --> pdb=" O PHE B1007 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE B1007 " --> pdb=" O LEU B1029 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY B1031 " --> pdb=" O ASN B1005 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 21 removed outlier: 3.790A pdb=" N GLY B 17 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU B 39 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU B 54 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE B 41 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 67 removed outlier: 4.193A pdb=" N ASN B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ALA B 86 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N HIS B 105 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 88 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 94 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 97 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N GLN F 45 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG B 103 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE F 47 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS B 105 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N THR F 49 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ASN B 107 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS B 153 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.896A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 218 through 221 removed outlier: 3.654A pdb=" N MET B 218 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 258 through 263 removed outlier: 6.883A pdb=" N GLY B 274 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N HIS B 261 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 272 " --> pdb=" O HIS B 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 279 through 289 removed outlier: 6.880A pdb=" N LEU B 280 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 299 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU B 288 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEU B 297 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 313 through 316 removed outlier: 3.519A pdb=" N GLU B 351 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS B 335 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA B 349 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AB8, first strand: chain 'B' and resid 721 through 727 removed outlier: 3.935A pdb=" N LYS B 723 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 794 " --> pdb=" O PHE B 733 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 791 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA B 804 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 793 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 750 through 751 Processing sheet with id=AC1, first strand: chain 'B' and resid 815 through 819 removed outlier: 7.281A pdb=" N VAL B 850 " --> pdb=" O VAL B 861 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 859 " --> pdb=" O GLN B 852 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 870 through 876 removed outlier: 4.125A pdb=" N SER B 872 " --> pdb=" O SER B 883 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 880 " --> pdb=" O TYR B 891 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 888 " --> pdb=" O ASN B 904 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN B 904 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 890 " --> pdb=" O GLU B 902 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 913 through 917 removed outlier: 3.862A pdb=" N ALA B 946 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA B 934 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLU B 944 " --> pdb=" O ALA B 934 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS B 936 " --> pdb=" O PHE B 942 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE B 942 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 954 through 959 removed outlier: 6.701A pdb=" N ALA B 968 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL B 957 " --> pdb=" O LEU B 966 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B 966 " --> pdb=" O VAL B 957 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE B 959 " --> pdb=" O ASN B 964 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASN B 964 " --> pdb=" O ILE B 959 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 975 " --> pdb=" O GLY B 967 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 973 " --> pdb=" O GLU B 969 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 974 " --> pdb=" O LEU B 997 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU B 997 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL B 976 " --> pdb=" O VAL B 995 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 582 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: 1.20 Time building geometry restraints manager: 0.87 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: 2658 1.34 - 1.46: 1900 1.46 - 1.58: 3541 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 8153 Sorted by residual: bond pdb=" N ALA B 249 " pdb=" CA ALA B 249 " ideal model delta sigma weight residual 1.464 1.455 0.009 9.80e-03 1.04e+04 8.21e-01 bond pdb=" N PRO A 527 " pdb=" CA PRO A 527 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.65e-01 bond pdb=" N ASP A 252 " pdb=" CA ASP A 252 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 7.34e-01 bond pdb=" CA ILE A 251 " pdb=" CB ILE A 251 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.34e-02 5.57e+03 6.97e-01 bond pdb=" CB TRP B1047 " pdb=" CG TRP B1047 " ideal model delta sigma weight residual 1.498 1.474 0.024 3.10e-02 1.04e+03 6.12e-01 ... (remaining 8148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 11013 2.20 - 4.40: 99 4.40 - 6.60: 8 6.60 - 8.80: 2 8.80 - 11.00: 1 Bond angle restraints: 11123 Sorted by residual: angle pdb=" C ASN A 136 " pdb=" CA ASN A 136 " pdb=" CB ASN A 136 " ideal model delta sigma weight residual 115.89 110.49 5.40 1.32e+00 5.74e-01 1.67e+01 angle pdb=" C GLU A 56 " pdb=" CA GLU A 56 " pdb=" CB GLU A 56 " ideal model delta sigma weight residual 115.89 110.92 4.97 1.32e+00 5.74e-01 1.42e+01 angle pdb=" CB MET B 938 " pdb=" CG MET B 938 " pdb=" SD MET B 938 " ideal model delta sigma weight residual 112.70 123.70 -11.00 3.00e+00 1.11e-01 1.34e+01 angle pdb=" N VAL A 55 " pdb=" CA VAL A 55 " pdb=" C VAL A 55 " ideal model delta sigma weight residual 112.80 108.70 4.10 1.15e+00 7.56e-01 1.27e+01 angle pdb=" C ASN B 885 " pdb=" CA ASN B 885 " pdb=" CB ASN B 885 " ideal model delta sigma weight residual 110.42 115.77 -5.35 1.99e+00 2.53e-01 7.23e+00 ... (remaining 11118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4239 17.88 - 35.75: 419 35.75 - 53.63: 100 53.63 - 71.50: 16 71.50 - 89.38: 5 Dihedral angle restraints: 4779 sinusoidal: 1484 harmonic: 3295 Sorted by residual: dihedral pdb=" CA GLY A 495 " pdb=" C GLY A 495 " pdb=" N LEU A 496 " pdb=" CA LEU A 496 " ideal model delta harmonic sigma weight residual 180.00 161.12 18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA TYR B 828 " pdb=" C TYR B 828 " pdb=" N PHE B 829 " pdb=" CA PHE B 829 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CG ARG B 103 " pdb=" CD ARG B 103 " pdb=" NE ARG B 103 " pdb=" CZ ARG B 103 " ideal model delta sinusoidal sigma weight residual -90.00 -132.92 42.92 2 1.50e+01 4.44e-03 9.89e+00 ... (remaining 4776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 736 0.029 - 0.057: 377 0.057 - 0.086: 100 0.086 - 0.115: 102 0.115 - 0.143: 23 Chirality restraints: 1338 Sorted by residual: chirality pdb=" CA ILE B 230 " pdb=" N ILE B 230 " pdb=" C ILE B 230 " pdb=" CB ILE B 230 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA VAL B 219 " pdb=" N VAL B 219 " pdb=" C VAL B 219 " pdb=" CB VAL B 219 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE B 220 " pdb=" N ILE B 220 " pdb=" C ILE B 220 " pdb=" CB ILE B 220 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1335 not shown) Planarity restraints: 1433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 184 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO B 185 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 245 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 246 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 523 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 524 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 524 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 524 " -0.020 5.00e-02 4.00e+02 ... (remaining 1430 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1210 2.76 - 3.30: 6844 3.30 - 3.83: 11807 3.83 - 4.37: 12959 4.37 - 4.90: 24495 Nonbonded interactions: 57315 Sorted by model distance: nonbonded pdb=" O LYS A 31 " pdb=" OG1 THR A 34 " model vdw 2.228 3.040 nonbonded pdb=" NH1 ARG B 739 " pdb=" OG SER B 757 " model vdw 2.250 3.120 nonbonded pdb=" ND1 HIS B 22 " pdb=" O ASP B 28 " model vdw 2.270 3.120 nonbonded pdb=" O THR B 102 " pdb=" OG1 THR B 102 " model vdw 2.305 3.040 nonbonded pdb=" OE1 GLU B 90 " pdb=" NH2 ARG B 103 " model vdw 2.317 3.120 ... (remaining 57310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 0.024 8153 Z= 0.151 Angle : 0.567 11.000 11123 Z= 0.316 Chirality : 0.045 0.143 1338 Planarity : 0.004 0.054 1433 Dihedral : 15.497 89.379 2645 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.32 % Favored : 93.59 % Rotamer: Outliers : 0.44 % Allowed : 27.45 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.61 (0.24), residues: 1108 helix: -2.64 (0.50), residues: 92 sheet: -0.87 (0.27), residues: 381 loop : -2.21 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 198 TYR 0.012 0.001 TYR B 812 PHE 0.020 0.001 PHE A 525 TRP 0.015 0.001 TRP A 36 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8153) covalent geometry : angle 0.56708 (11123) hydrogen bonds : bond 0.11315 ( 235) hydrogen bonds : angle 6.50596 ( 582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 54 ASN cc_start: 0.8470 (m-40) cc_final: 0.8216 (t0) outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 0.0560 time to fit residues: 5.1597 Evaluate side-chains 65 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain F residue 4 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.0770 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 10.0000 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS B 950 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.076577 restraints weight = 21661.620| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 4.05 r_work: 0.3109 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.0579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8153 Z= 0.081 Angle : 0.458 5.607 11123 Z= 0.244 Chirality : 0.044 0.137 1338 Planarity : 0.003 0.055 1433 Dihedral : 4.232 44.531 1207 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.40 % Rotamer: Outliers : 2.34 % Allowed : 25.26 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.47 (0.24), residues: 1108 helix: -2.37 (0.52), residues: 92 sheet: -0.71 (0.27), residues: 379 loop : -2.19 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 198 TYR 0.008 0.001 TYR B1114 PHE 0.012 0.001 PHE A 525 TRP 0.012 0.001 TRP B 893 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00175 ( 8153) covalent geometry : angle 0.45761 (11123) hydrogen bonds : bond 0.02985 ( 235) hydrogen bonds : angle 5.52889 ( 582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.228 Fit side-chains REVERT: A 54 ASN cc_start: 0.8418 (m-40) cc_final: 0.7906 (t0) REVERT: A 197 ASP cc_start: 0.6684 (t70) cc_final: 0.6273 (t70) REVERT: B 315 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.9032 (p) outliers start: 16 outliers final: 4 residues processed: 77 average time/residue: 0.0649 time to fit residues: 7.5199 Evaluate side-chains 71 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 4 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.0020 chunk 104 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2132 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.095378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.075554 restraints weight = 21628.192| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.92 r_work: 0.3085 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8153 Z= 0.146 Angle : 0.486 6.532 11123 Z= 0.257 Chirality : 0.044 0.139 1338 Planarity : 0.003 0.053 1433 Dihedral : 4.051 44.686 1202 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.77 % Favored : 93.14 % Rotamer: Outliers : 2.92 % Allowed : 25.11 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.42 (0.24), residues: 1108 helix: -2.15 (0.54), residues: 90 sheet: -0.74 (0.27), residues: 378 loop : -2.14 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 198 TYR 0.012 0.001 TYR B 91 PHE 0.011 0.001 PHE B 155 TRP 0.024 0.002 TRP A 36 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8153) covalent geometry : angle 0.48588 (11123) hydrogen bonds : bond 0.03306 ( 235) hydrogen bonds : angle 5.45876 ( 582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.255 Fit side-chains REVERT: A 54 ASN cc_start: 0.8492 (m-40) cc_final: 0.8018 (t0) REVERT: A 197 ASP cc_start: 0.6903 (t70) cc_final: 0.6453 (t70) REVERT: B 130 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8337 (ptp) REVERT: B 1062 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8594 (mp) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.0653 time to fit residues: 7.6563 Evaluate side-chains 79 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.095293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.074561 restraints weight = 22150.227| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.13 r_work: 0.3072 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8153 Z= 0.128 Angle : 0.471 4.472 11123 Z= 0.250 Chirality : 0.044 0.139 1338 Planarity : 0.003 0.052 1433 Dihedral : 4.064 49.446 1202 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.14 % Favored : 93.77 % Rotamer: Outliers : 3.50 % Allowed : 25.55 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.35 (0.24), residues: 1108 helix: -2.01 (0.55), residues: 90 sheet: -0.67 (0.27), residues: 370 loop : -2.10 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 198 TYR 0.011 0.001 TYR B 91 PHE 0.017 0.001 PHE A 525 TRP 0.016 0.002 TRP A 36 HIS 0.002 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8153) covalent geometry : angle 0.47083 (11123) hydrogen bonds : bond 0.03110 ( 235) hydrogen bonds : angle 5.41394 ( 582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.315 Fit side-chains REVERT: A 19 ILE cc_start: 0.9244 (mm) cc_final: 0.9024 (mm) REVERT: A 54 ASN cc_start: 0.8458 (m-40) cc_final: 0.7908 (t0) REVERT: A 197 ASP cc_start: 0.6600 (t70) cc_final: 0.6175 (t70) REVERT: B 1062 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8512 (mp) outliers start: 24 outliers final: 16 residues processed: 81 average time/residue: 0.0667 time to fit residues: 8.1478 Evaluate side-chains 81 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1107 GLU Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 60 optimal weight: 0.0170 overall best weight: 0.8278 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.095586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.075197 restraints weight = 21743.274| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.03 r_work: 0.3086 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8153 Z= 0.111 Angle : 0.468 7.296 11123 Z= 0.247 Chirality : 0.044 0.138 1338 Planarity : 0.003 0.051 1433 Dihedral : 4.022 54.521 1202 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.50 % Favored : 93.41 % Rotamer: Outliers : 3.36 % Allowed : 25.99 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.25 (0.24), residues: 1108 helix: -2.03 (0.54), residues: 90 sheet: -0.67 (0.27), residues: 378 loop : -1.99 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 198 TYR 0.011 0.001 TYR B 91 PHE 0.012 0.001 PHE A 525 TRP 0.028 0.002 TRP A 36 HIS 0.002 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8153) covalent geometry : angle 0.46786 (11123) hydrogen bonds : bond 0.02894 ( 235) hydrogen bonds : angle 5.28478 ( 582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.258 Fit side-chains REVERT: A 19 ILE cc_start: 0.9261 (mm) cc_final: 0.9020 (mm) REVERT: A 54 ASN cc_start: 0.8536 (m-40) cc_final: 0.7978 (t0) REVERT: A 197 ASP cc_start: 0.6796 (t70) cc_final: 0.6360 (t70) outliers start: 23 outliers final: 14 residues processed: 81 average time/residue: 0.0558 time to fit residues: 6.9190 Evaluate side-chains 77 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1107 GLU Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 76 optimal weight: 0.0770 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.094736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074474 restraints weight = 21850.642| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 4.09 r_work: 0.3052 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8153 Z= 0.147 Angle : 0.492 4.488 11123 Z= 0.261 Chirality : 0.044 0.138 1338 Planarity : 0.003 0.050 1433 Dihedral : 4.145 59.196 1202 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.77 % Favored : 93.14 % Rotamer: Outliers : 3.50 % Allowed : 25.69 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.25 (0.24), residues: 1108 helix: -1.93 (0.54), residues: 90 sheet: -0.66 (0.27), residues: 376 loop : -2.01 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 198 TYR 0.012 0.001 TYR B 91 PHE 0.017 0.001 PHE A 525 TRP 0.034 0.002 TRP A 36 HIS 0.002 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8153) covalent geometry : angle 0.49183 (11123) hydrogen bonds : bond 0.03169 ( 235) hydrogen bonds : angle 5.33587 ( 582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.281 Fit side-chains REVERT: A 19 ILE cc_start: 0.9252 (mm) cc_final: 0.9022 (mm) REVERT: A 54 ASN cc_start: 0.8500 (m-40) cc_final: 0.7989 (t0) REVERT: A 197 ASP cc_start: 0.6831 (t70) cc_final: 0.6379 (t70) REVERT: B 207 TRP cc_start: 0.8760 (OUTLIER) cc_final: 0.7863 (p-90) outliers start: 24 outliers final: 20 residues processed: 78 average time/residue: 0.0652 time to fit residues: 7.8017 Evaluate side-chains 82 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1107 GLU Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 49 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 72 optimal weight: 0.0030 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 0.0170 chunk 39 optimal weight: 0.9980 overall best weight: 0.7430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074419 restraints weight = 21578.395| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 4.12 r_work: 0.3075 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8153 Z= 0.103 Angle : 0.459 4.784 11123 Z= 0.244 Chirality : 0.044 0.136 1338 Planarity : 0.003 0.051 1433 Dihedral : 3.976 56.004 1202 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 2.77 % Allowed : 26.13 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.15 (0.24), residues: 1108 helix: -1.80 (0.56), residues: 90 sheet: -0.61 (0.27), residues: 376 loop : -1.94 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 198 TYR 0.010 0.001 TYR B 91 PHE 0.016 0.001 PHE A 525 TRP 0.020 0.002 TRP A 36 HIS 0.002 0.000 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8153) covalent geometry : angle 0.45889 (11123) hydrogen bonds : bond 0.02787 ( 235) hydrogen bonds : angle 5.19785 ( 582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.9232 (mm) cc_final: 0.8991 (mm) REVERT: A 54 ASN cc_start: 0.8629 (m-40) cc_final: 0.8108 (t0) REVERT: A 197 ASP cc_start: 0.6874 (t70) cc_final: 0.6418 (t70) REVERT: B 207 TRP cc_start: 0.8716 (OUTLIER) cc_final: 0.7848 (p-90) outliers start: 19 outliers final: 16 residues processed: 78 average time/residue: 0.0527 time to fit residues: 6.5410 Evaluate side-chains 81 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1107 GLU Chi-restraints excluded: chain F residue 4 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 0.0270 chunk 45 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 chunk 5 optimal weight: 0.0770 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 104 optimal weight: 0.3980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.097512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077332 restraints weight = 21845.984| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 4.13 r_work: 0.3113 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8153 Z= 0.074 Angle : 0.438 4.459 11123 Z= 0.232 Chirality : 0.043 0.137 1338 Planarity : 0.003 0.052 1433 Dihedral : 3.715 52.340 1202 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 2.48 % Allowed : 26.86 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.00 (0.25), residues: 1108 helix: -1.70 (0.56), residues: 90 sheet: -0.56 (0.27), residues: 392 loop : -1.81 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 198 TYR 0.008 0.001 TYR B 91 PHE 0.015 0.001 PHE A 525 TRP 0.039 0.002 TRP A 36 HIS 0.003 0.000 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00162 ( 8153) covalent geometry : angle 0.43758 (11123) hydrogen bonds : bond 0.02386 ( 235) hydrogen bonds : angle 4.93742 ( 582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.9220 (mm) cc_final: 0.8961 (mm) REVERT: A 54 ASN cc_start: 0.8639 (m-40) cc_final: 0.8122 (t0) REVERT: A 197 ASP cc_start: 0.6872 (t70) cc_final: 0.6434 (t70) REVERT: B 207 TRP cc_start: 0.8614 (OUTLIER) cc_final: 0.7768 (p-90) outliers start: 17 outliers final: 13 residues processed: 79 average time/residue: 0.0695 time to fit residues: 8.4852 Evaluate side-chains 79 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1107 GLU Chi-restraints excluded: chain F residue 4 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 17 optimal weight: 30.0000 chunk 82 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 0.0020 chunk 111 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 overall best weight: 0.5086 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.097085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076771 restraints weight = 21638.559| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 4.01 r_work: 0.3122 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8153 Z= 0.085 Angle : 0.447 5.713 11123 Z= 0.236 Chirality : 0.044 0.136 1338 Planarity : 0.003 0.052 1433 Dihedral : 3.668 50.325 1202 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.68 % Rotamer: Outliers : 2.34 % Allowed : 27.30 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.94 (0.25), residues: 1108 helix: -1.58 (0.57), residues: 90 sheet: -0.52 (0.27), residues: 385 loop : -1.78 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 198 TYR 0.009 0.001 TYR B 136 PHE 0.021 0.001 PHE A 525 TRP 0.042 0.002 TRP A 36 HIS 0.002 0.000 HIS B 261 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 8153) covalent geometry : angle 0.44686 (11123) hydrogen bonds : bond 0.02551 ( 235) hydrogen bonds : angle 4.88843 ( 582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.9217 (mm) cc_final: 0.8976 (mm) REVERT: A 54 ASN cc_start: 0.8618 (m-40) cc_final: 0.8100 (t0) REVERT: A 197 ASP cc_start: 0.6811 (t70) cc_final: 0.6373 (t70) REVERT: B 207 TRP cc_start: 0.8632 (OUTLIER) cc_final: 0.7758 (p-90) outliers start: 16 outliers final: 13 residues processed: 79 average time/residue: 0.0674 time to fit residues: 8.2221 Evaluate side-chains 79 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1107 GLU Chi-restraints excluded: chain F residue 4 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.096539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.076185 restraints weight = 21741.696| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 4.02 r_work: 0.3110 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8153 Z= 0.105 Angle : 0.457 6.003 11123 Z= 0.241 Chirality : 0.044 0.143 1338 Planarity : 0.003 0.052 1433 Dihedral : 3.681 47.503 1202 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 2.34 % Allowed : 27.30 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.25), residues: 1108 helix: -1.59 (0.57), residues: 90 sheet: -0.51 (0.27), residues: 385 loop : -1.76 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 198 TYR 0.010 0.001 TYR B 91 PHE 0.022 0.001 PHE A 525 TRP 0.032 0.002 TRP A 36 HIS 0.002 0.000 HIS B 261 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8153) covalent geometry : angle 0.45745 (11123) hydrogen bonds : bond 0.02734 ( 235) hydrogen bonds : angle 4.91357 ( 582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.9196 (mm) cc_final: 0.8989 (mm) REVERT: A 54 ASN cc_start: 0.8647 (m-40) cc_final: 0.8139 (t0) REVERT: A 197 ASP cc_start: 0.6862 (t70) cc_final: 0.6413 (t70) REVERT: B 207 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.7697 (p-90) outliers start: 16 outliers final: 14 residues processed: 77 average time/residue: 0.0683 time to fit residues: 8.2169 Evaluate side-chains 80 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1107 GLU Chi-restraints excluded: chain F residue 4 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 0.0030 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 107 optimal weight: 0.0000 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** B 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.094644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074320 restraints weight = 21715.120| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 4.03 r_work: 0.3073 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8153 Z= 0.165 Angle : 0.505 6.571 11123 Z= 0.267 Chirality : 0.045 0.139 1338 Planarity : 0.003 0.051 1433 Dihedral : 3.949 43.655 1202 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.31 % Favored : 92.60 % Rotamer: Outliers : 2.34 % Allowed : 27.45 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.25), residues: 1108 helix: -1.73 (0.55), residues: 90 sheet: -0.58 (0.27), residues: 391 loop : -1.84 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 198 TYR 0.014 0.001 TYR B 91 PHE 0.021 0.001 PHE A 525 TRP 0.048 0.003 TRP A 36 HIS 0.003 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8153) covalent geometry : angle 0.50541 (11123) hydrogen bonds : bond 0.03309 ( 235) hydrogen bonds : angle 5.20066 ( 582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.82 seconds wall clock time: 32 minutes 53.95 seconds (1973.95 seconds total)