Starting phenix.real_space_refine on Wed Feb 4 01:34:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ltl_63372/02_2026/9ltl_63372.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ltl_63372/02_2026/9ltl_63372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ltl_63372/02_2026/9ltl_63372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ltl_63372/02_2026/9ltl_63372.map" model { file = "/net/cci-nas-00/data/ceres_data/9ltl_63372/02_2026/9ltl_63372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ltl_63372/02_2026/9ltl_63372.cif" } resolution = 2.93 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= 0.032 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 36 5.16 5 C 5175 2.51 5 N 1414 2.21 5 O 1430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 8055 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2075 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 8, 'TRANS': 294} Chain breaks: 8 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 8, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 6, 'ASP:plan': 13, 'TYR:plan': 4, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 255 Chain: "B" Number of atoms: 5654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5654 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 747} Chain breaks: 5 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 37, 'ARG:plan': 5, 'ASP:plan': 23, 'ASN:plan1': 4, 'GLN:plan1': 7, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 306 Chain: "F" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 326 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 1.94, per 1000 atoms: 0.24 Number of scatterers: 8055 At special positions: 0 Unit cell: (94.35, 110.5, 90.95, 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 36 16.00 O 1430 8.00 N 1414 7.00 C 5175 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: 0.74 Conformation dependent library (CDL) restraints added in 374.0 milliseconds 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 22 sheets defined 7.8% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 17 through 28 removed outlier: 3.536A pdb=" N ARG A 21 " --> pdb=" O ASN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.548A pdb=" N PHE A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.632A 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 1062 removed outlier: 3.762A pdb=" N TYR B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN B1049 " --> pdb=" O GLU B1045 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B1057 " --> pdb=" O ASP B1053 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B1059 " --> pdb=" O GLN B1055 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS B1060 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B1061 " --> pdb=" O ARG B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1074 Processing helix chain 'B' and resid 1091 through 1097 removed outlier: 3.702A pdb=" N GLU B1095 " --> pdb=" O GLY B1091 " (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 1107 removed outlier: 3.872A pdb=" N GLU B1107 " --> pdb=" O PRO B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1136 removed outlier: 3.965A pdb=" N LEU B1136 " --> pdb=" O VAL B1132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.687A pdb=" N ALA A 529 " --> pdb=" O HIS A 544 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 75 removed outlier: 3.673A pdb=" N PHE A 72 " --> pdb=" O TYR A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.604A pdb=" N ILE A 195 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A 205 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA5, first strand: chain 'A' and resid 466 through 468 Processing sheet with id=AA6, first strand: chain 'B' and resid 1004 through 1009 removed outlier: 6.789A pdb=" N GLY B1031 " --> pdb=" O ASN B1005 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE B1007 " --> pdb=" O LEU B1029 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU B1029 " --> pdb=" O PHE B1007 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B1030 " --> pdb=" O GLY B1038 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 17 through 21 removed outlier: 4.790A pdb=" N LEU B 29 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU B 39 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU B 54 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE B 41 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 61 through 67 removed outlier: 4.180A pdb=" N ASN B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA B 86 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N HIS B 105 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE B 88 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N GLN F 45 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG B 103 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE F 47 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS B 105 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N THR F 49 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N ASN B 107 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU B 152 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 169 removed outlier: 5.991A pdb=" N VAL B 164 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN B 183 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 166 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 169 removed outlier: 5.991A pdb=" N VAL B 164 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN B 183 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 166 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 218 through 221 removed outlier: 3.614A pdb=" N MET B 218 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 258 through 263 removed outlier: 7.010A pdb=" N GLY B 274 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS B 261 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 272 " --> pdb=" O HIS B 261 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG B 263 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ARG B 270 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 273 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 275 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 280 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP B 299 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLU B 288 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU B 297 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 313 through 318 removed outlier: 6.683A pdb=" N VAL B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER B 331 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR B 352 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 333 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 361 through 363 removed outlier: 4.285A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 721 through 727 removed outlier: 3.986A pdb=" N LYS B 723 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 794 " --> pdb=" O PHE B 733 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LEU B 791 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA B 804 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 793 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER B 764 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 740 through 742 Processing sheet with id=AB8, first strand: chain 'B' and resid 811 through 819 removed outlier: 6.088A pdb=" N GLY B 832 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU B 816 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 830 " --> pdb=" O LEU B 816 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER B 818 " --> pdb=" O TYR B 828 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR B 828 " --> pdb=" O SER B 818 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 831 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 849 " --> pdb=" O VAL B 831 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 850 " --> pdb=" O VAL B 861 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 859 " --> pdb=" O GLN B 852 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 874 through 876 removed outlier: 6.630A pdb=" N VAL B 888 " --> pdb=" O ASN B 904 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN B 904 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 890 " --> pdb=" O GLU B 902 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 911 through 917 removed outlier: 6.843A pdb=" N ALA B 934 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLU B 944 " --> pdb=" O ALA B 934 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 957 through 959 removed outlier: 6.931A pdb=" N LEU B 974 " --> pdb=" O LEU B 997 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU B 997 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL B 976 " --> pdb=" O VAL B 995 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1076 through 1077 Processing sheet with id=AC4, first strand: chain 'B' and resid 1113 through 1114 245 hydrogen bonds defined for protein. 618 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: 1.71 Time building geometry restraints manager: 0.98 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: 1906 1.46 - 1.58: 3589 1.58 - 1.70: 1 1.70 - 1.82: 53 Bond restraints: 8207 Sorted by residual: bond pdb=" CB PRO A 524 " pdb=" CG PRO A 524 " ideal model delta sigma weight residual 1.492 1.626 -0.134 5.00e-02 4.00e+02 7.18e+00 bond pdb=" CA PRO A 527 " pdb=" C PRO A 527 " ideal model delta sigma weight residual 1.527 1.514 0.013 1.07e-02 8.73e+03 1.54e+00 bond pdb=" C VAL B 324 " pdb=" N GLY B 325 " ideal model delta sigma weight residual 1.332 1.327 0.006 5.00e-03 4.00e+04 1.23e+00 bond pdb=" N ILE A 231 " pdb=" CA ILE A 231 " ideal model delta sigma weight residual 1.474 1.459 0.015 1.57e-02 4.06e+03 9.70e-01 bond pdb=" CA LEU A 105 " pdb=" C LEU A 105 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.08e-02 8.57e+03 9.49e-01 ... (remaining 8202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 11003 1.97 - 3.94: 150 3.94 - 5.91: 17 5.91 - 7.88: 1 7.88 - 9.85: 2 Bond angle restraints: 11173 Sorted by residual: angle pdb=" CA PRO A 524 " pdb=" N PRO A 524 " pdb=" CD PRO A 524 " ideal model delta sigma weight residual 112.00 102.15 9.85 1.40e+00 5.10e-01 4.95e+01 angle pdb=" N VAL A 114 " pdb=" CA VAL A 114 " pdb=" C VAL A 114 " ideal model delta sigma weight residual 112.83 107.74 5.09 9.90e-01 1.02e+00 2.65e+01 angle pdb=" N ILE A 116 " pdb=" CA ILE A 116 " pdb=" C ILE A 116 " ideal model delta sigma weight residual 111.91 107.95 3.96 8.90e-01 1.26e+00 1.98e+01 angle pdb=" N ILE A 231 " pdb=" CA ILE A 231 " pdb=" C ILE A 231 " ideal model delta sigma weight residual 106.21 110.85 -4.64 1.07e+00 8.73e-01 1.88e+01 angle pdb=" C ASN A 136 " pdb=" CA ASN A 136 " pdb=" CB ASN A 136 " ideal model delta sigma weight residual 115.89 110.39 5.50 1.32e+00 5.74e-01 1.74e+01 ... (remaining 11168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 4227 18.02 - 36.04: 465 36.04 - 54.06: 104 54.06 - 72.08: 19 72.08 - 90.10: 5 Dihedral angle restraints: 4820 sinusoidal: 1577 harmonic: 3243 Sorted by residual: dihedral pdb=" CA THR B1041 " pdb=" C THR B1041 " pdb=" N SER B1042 " pdb=" CA SER B1042 " ideal model delta harmonic sigma weight residual -180.00 -158.99 -21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CB GLU B 958 " pdb=" CG GLU B 958 " pdb=" CD GLU B 958 " pdb=" OE1 GLU B 958 " ideal model delta sinusoidal sigma weight residual 0.00 90.10 -90.10 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CA ASP B 925 " pdb=" CB ASP B 925 " pdb=" CG ASP B 925 " pdb=" OD1 ASP B 925 " ideal model delta sinusoidal sigma weight residual -30.00 -83.73 53.73 1 2.00e+01 2.50e-03 9.80e+00 ... (remaining 4817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 738 0.029 - 0.058: 372 0.058 - 0.087: 101 0.087 - 0.116: 98 0.116 - 0.145: 17 Chirality restraints: 1326 Sorted by residual: chirality pdb=" CA ILE B 959 " pdb=" N ILE B 959 " pdb=" C ILE B 959 " pdb=" CB ILE B 959 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-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 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE B 237 " pdb=" N ILE B 237 " pdb=" C ILE B 237 " pdb=" CB ILE B 237 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1323 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 523 " -0.076 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO A 524 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 524 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 524 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 250 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO B 251 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 251 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 251 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 184 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO B 185 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " -0.017 5.00e-02 4.00e+02 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 504 2.73 - 3.27: 7513 3.27 - 3.81: 12283 3.81 - 4.36: 14344 4.36 - 4.90: 26011 Nonbonded interactions: 60655 Sorted by model distance: nonbonded pdb=" OG1 THR B 177 " pdb=" OE1 GLU B 194 " model vdw 2.186 3.040 nonbonded pdb=" OG SER B 116 " pdb=" O GLY B 119 " model vdw 2.259 3.040 nonbonded pdb=" OG SER B 326 " pdb=" O GLY B 329 " model vdw 2.260 3.040 nonbonded pdb=" OE1 GLU B 40 " pdb=" OH TYR B 42 " model vdw 2.272 3.040 nonbonded pdb=" O ILE B 359 " pdb=" ND2 ASN B1005 " model vdw 2.274 3.120 ... (remaining 60650 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: 2.930 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.620 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:8.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 0.134 8207 Z= 0.145 Angle : 0.596 9.848 11173 Z= 0.347 Chirality : 0.044 0.145 1326 Planarity : 0.004 0.109 1437 Dihedral : 16.300 90.101 2720 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.91 % Favored : 91.90 % Rotamer: Outliers : 0.14 % Allowed : 29.48 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.79 (0.24), residues: 1087 helix: -2.71 (0.55), residues: 73 sheet: -1.26 (0.27), residues: 404 loop : -2.19 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 18 TYR 0.014 0.001 TYR A 223 PHE 0.011 0.001 PHE A 525 TRP 0.013 0.002 TRP A 36 HIS 0.003 0.001 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8207) covalent geometry : angle 0.59644 (11173) hydrogen bonds : bond 0.13782 ( 234) hydrogen bonds : angle 7.11565 ( 618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 36 TRP cc_start: 0.7474 (t60) cc_final: 0.7252 (t60) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.4290 time to fit residues: 32.4572 Evaluate side-chains 64 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.1980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.105348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.088126 restraints weight = 24229.315| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 4.16 r_work: 0.3495 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8207 Z= 0.139 Angle : 0.534 6.298 11173 Z= 0.284 Chirality : 0.044 0.140 1326 Planarity : 0.004 0.053 1437 Dihedral : 4.285 23.120 1186 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.18 % Favored : 92.64 % Rotamer: Outliers : 3.03 % Allowed : 27.27 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.72 (0.24), residues: 1087 helix: -2.60 (0.54), residues: 73 sheet: -1.14 (0.27), residues: 400 loop : -2.21 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 18 TYR 0.015 0.001 TYR F 35 PHE 0.015 0.001 PHE A 528 TRP 0.008 0.001 TRP A 36 HIS 0.002 0.001 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8207) covalent geometry : angle 0.53434 (11173) hydrogen bonds : bond 0.03342 ( 234) hydrogen bonds : angle 5.75175 ( 618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.314 Fit side-chains REVERT: A 36 TRP cc_start: 0.7699 (t60) cc_final: 0.7470 (t60) REVERT: B 244 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7068 (ttpp) outliers start: 22 outliers final: 6 residues processed: 86 average time/residue: 0.3418 time to fit residues: 31.9996 Evaluate side-chains 73 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.102924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.085846 restraints weight = 23491.826| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.95 r_work: 0.3455 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8207 Z= 0.212 Angle : 0.589 6.752 11173 Z= 0.312 Chirality : 0.045 0.165 1326 Planarity : 0.004 0.052 1437 Dihedral : 4.516 22.964 1185 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.56 % Favored : 91.26 % Rotamer: Outliers : 3.58 % Allowed : 28.79 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.72 (0.24), residues: 1087 helix: -2.71 (0.51), residues: 73 sheet: -1.20 (0.27), residues: 404 loop : -2.15 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 198 TYR 0.014 0.002 TYR B 5 PHE 0.013 0.001 PHE B1003 TRP 0.007 0.001 TRP B 207 HIS 0.003 0.001 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 8207) covalent geometry : angle 0.58904 (11173) hydrogen bonds : bond 0.03716 ( 234) hydrogen bonds : angle 5.89384 ( 618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.283 Fit side-chains REVERT: A 36 TRP cc_start: 0.7736 (t60) cc_final: 0.7497 (t60) REVERT: A 462 ASP cc_start: 0.8445 (t0) cc_final: 0.8129 (t0) REVERT: B 193 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.7362 (m-10) REVERT: B 244 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7174 (ttpp) outliers start: 26 outliers final: 9 residues processed: 90 average time/residue: 0.3124 time to fit residues: 30.8009 Evaluate side-chains 78 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 107 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 24 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.104520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.087325 restraints weight = 24529.590| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 4.13 r_work: 0.3474 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8207 Z= 0.132 Angle : 0.539 8.127 11173 Z= 0.283 Chirality : 0.044 0.142 1326 Planarity : 0.004 0.051 1437 Dihedral : 4.349 22.876 1185 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.27 % Favored : 92.55 % Rotamer: Outliers : 4.13 % Allowed : 29.06 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.60 (0.24), residues: 1087 helix: -2.48 (0.53), residues: 73 sheet: -1.05 (0.28), residues: 396 loop : -2.13 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 18 TYR 0.014 0.001 TYR A 223 PHE 0.021 0.001 PHE A 525 TRP 0.007 0.001 TRP B 893 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8207) covalent geometry : angle 0.53894 (11173) hydrogen bonds : bond 0.03121 ( 234) hydrogen bonds : angle 5.59738 ( 618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.253 Fit side-chains REVERT: A 36 TRP cc_start: 0.7718 (t60) cc_final: 0.7489 (t60) REVERT: A 462 ASP cc_start: 0.8409 (t0) cc_final: 0.8060 (t0) REVERT: B 244 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7061 (ttpp) REVERT: B 1068 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7949 (tt) outliers start: 30 outliers final: 7 residues processed: 94 average time/residue: 0.3166 time to fit residues: 32.4277 Evaluate side-chains 75 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 1068 ILE Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.2980 chunk 20 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.105355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.088137 restraints weight = 23433.621| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.99 r_work: 0.3506 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8207 Z= 0.111 Angle : 0.527 8.590 11173 Z= 0.276 Chirality : 0.044 0.140 1326 Planarity : 0.004 0.056 1437 Dihedral : 4.174 21.270 1185 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.27 % Favored : 92.55 % Rotamer: Outliers : 3.17 % Allowed : 28.79 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.46 (0.24), residues: 1087 helix: -2.27 (0.53), residues: 73 sheet: -0.99 (0.28), residues: 397 loop : -2.03 (0.22), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 198 TYR 0.009 0.001 TYR B 5 PHE 0.020 0.001 PHE A 528 TRP 0.008 0.001 TRP B 893 HIS 0.002 0.000 HIS B1077 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8207) covalent geometry : angle 0.52705 (11173) hydrogen bonds : bond 0.02886 ( 234) hydrogen bonds : angle 5.35662 ( 618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.323 Fit side-chains REVERT: A 462 ASP cc_start: 0.8441 (t0) cc_final: 0.8107 (t0) REVERT: B 244 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7085 (ttpp) outliers start: 23 outliers final: 11 residues processed: 89 average time/residue: 0.3688 time to fit residues: 36.0198 Evaluate side-chains 76 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1059 ASN Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 110 optimal weight: 0.0470 chunk 71 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 0.0270 chunk 107 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.106720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.089625 restraints weight = 23264.069| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.99 r_work: 0.3538 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8207 Z= 0.093 Angle : 0.522 9.421 11173 Z= 0.270 Chirality : 0.044 0.142 1326 Planarity : 0.004 0.056 1437 Dihedral : 4.035 20.614 1185 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.62 % Favored : 93.19 % Rotamer: Outliers : 2.75 % Allowed : 29.06 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.36 (0.25), residues: 1087 helix: -2.10 (0.55), residues: 73 sheet: -0.92 (0.28), residues: 397 loop : -1.97 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 198 TYR 0.016 0.001 TYR A 223 PHE 0.015 0.001 PHE A 147 TRP 0.021 0.001 TRP A 36 HIS 0.002 0.000 HIS B1077 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 8207) covalent geometry : angle 0.52168 (11173) hydrogen bonds : bond 0.02670 ( 234) hydrogen bonds : angle 5.16178 ( 618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.328 Fit side-chains REVERT: A 462 ASP cc_start: 0.8422 (t0) cc_final: 0.8108 (t0) REVERT: B 244 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7058 (ttpp) REVERT: B 282 MET cc_start: 0.8108 (tpp) cc_final: 0.7890 (tpp) outliers start: 20 outliers final: 11 residues processed: 86 average time/residue: 0.3825 time to fit residues: 35.9625 Evaluate side-chains 79 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.105176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.088048 restraints weight = 23772.757| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 4.03 r_work: 0.3501 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8207 Z= 0.138 Angle : 0.548 10.177 11173 Z= 0.284 Chirality : 0.044 0.153 1326 Planarity : 0.004 0.057 1437 Dihedral : 4.122 20.649 1185 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.08 % Favored : 92.73 % Rotamer: Outliers : 3.72 % Allowed : 28.79 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.29 (0.25), residues: 1087 helix: -1.79 (0.58), residues: 67 sheet: -0.92 (0.28), residues: 393 loop : -1.93 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 198 TYR 0.010 0.001 TYR B 5 PHE 0.019 0.001 PHE A 528 TRP 0.018 0.001 TRP A 36 HIS 0.003 0.000 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8207) covalent geometry : angle 0.54751 (11173) hydrogen bonds : bond 0.02986 ( 234) hydrogen bonds : angle 5.26792 ( 618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.334 Fit side-chains REVERT: A 462 ASP cc_start: 0.8471 (t0) cc_final: 0.8127 (t0) REVERT: B 244 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7102 (ttpp) REVERT: B 282 MET cc_start: 0.8128 (tpp) cc_final: 0.7894 (tpp) REVERT: B 927 MET cc_start: 0.8459 (pmm) cc_final: 0.8205 (ptt) outliers start: 27 outliers final: 14 residues processed: 91 average time/residue: 0.3437 time to fit residues: 34.6770 Evaluate side-chains 81 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 0.0470 chunk 97 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.105348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.088196 restraints weight = 23389.898| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.02 r_work: 0.3506 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8207 Z= 0.127 Angle : 0.545 10.661 11173 Z= 0.280 Chirality : 0.044 0.153 1326 Planarity : 0.004 0.059 1437 Dihedral : 4.113 20.996 1185 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.81 % Favored : 93.01 % Rotamer: Outliers : 2.75 % Allowed : 29.89 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.24 (0.25), residues: 1087 helix: -1.56 (0.60), residues: 67 sheet: -0.93 (0.28), residues: 397 loop : -1.89 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 198 TYR 0.014 0.001 TYR A 223 PHE 0.015 0.001 PHE A 147 TRP 0.017 0.001 TRP A 36 HIS 0.002 0.000 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8207) covalent geometry : angle 0.54528 (11173) hydrogen bonds : bond 0.02902 ( 234) hydrogen bonds : angle 5.22766 ( 618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.365 Fit side-chains REVERT: A 462 ASP cc_start: 0.8468 (t0) cc_final: 0.8133 (t0) REVERT: B 244 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7089 (ttpp) REVERT: B 282 MET cc_start: 0.8133 (tpp) cc_final: 0.7904 (tpp) REVERT: F 50 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7132 (pp20) outliers start: 20 outliers final: 14 residues processed: 86 average time/residue: 0.3323 time to fit residues: 31.5131 Evaluate side-chains 85 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.105896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088636 restraints weight = 23386.958| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 4.06 r_work: 0.3513 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8207 Z= 0.115 Angle : 0.546 9.488 11173 Z= 0.281 Chirality : 0.044 0.143 1326 Planarity : 0.004 0.070 1437 Dihedral : 4.034 19.875 1185 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.36 % Favored : 92.46 % Rotamer: Outliers : 2.62 % Allowed : 30.17 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.18 (0.25), residues: 1087 helix: -1.31 (0.62), residues: 67 sheet: -0.89 (0.28), residues: 396 loop : -1.87 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 198 TYR 0.010 0.001 TYR A 460 PHE 0.020 0.001 PHE A 528 TRP 0.017 0.001 TRP A 36 HIS 0.002 0.000 HIS B1077 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8207) covalent geometry : angle 0.54590 (11173) hydrogen bonds : bond 0.02784 ( 234) hydrogen bonds : angle 5.15085 ( 618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.243 Fit side-chains REVERT: A 462 ASP cc_start: 0.8456 (t0) cc_final: 0.8127 (t0) REVERT: B 244 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7058 (ttpp) REVERT: B 282 MET cc_start: 0.8118 (tpp) cc_final: 0.7888 (tpp) REVERT: F 50 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7163 (pp20) outliers start: 19 outliers final: 14 residues processed: 86 average time/residue: 0.3227 time to fit residues: 30.4419 Evaluate side-chains 84 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 7.9990 chunk 105 optimal weight: 0.0070 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.103423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.086088 restraints weight = 23561.435| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 4.04 r_work: 0.3467 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8207 Z= 0.192 Angle : 0.603 9.749 11173 Z= 0.312 Chirality : 0.045 0.157 1326 Planarity : 0.004 0.077 1437 Dihedral : 4.413 21.389 1185 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.91 % Favored : 91.90 % Rotamer: Outliers : 3.03 % Allowed : 29.61 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.37 (0.25), residues: 1087 helix: -1.69 (0.58), residues: 73 sheet: -1.06 (0.28), residues: 401 loop : -1.94 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 198 TYR 0.018 0.001 TYR A 460 PHE 0.013 0.001 PHE B1003 TRP 0.013 0.001 TRP A 36 HIS 0.003 0.001 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8207) covalent geometry : angle 0.60276 (11173) hydrogen bonds : bond 0.03402 ( 234) hydrogen bonds : angle 5.46632 ( 618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 462 ASP cc_start: 0.8469 (t0) cc_final: 0.8110 (t0) REVERT: B 244 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7169 (ttpp) REVERT: F 50 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7141 (pp20) outliers start: 22 outliers final: 14 residues processed: 84 average time/residue: 0.3311 time to fit residues: 30.5185 Evaluate side-chains 80 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.0470 chunk 2 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.105885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.088851 restraints weight = 23222.555| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.95 r_work: 0.3524 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8207 Z= 0.106 Angle : 0.567 10.100 11173 Z= 0.290 Chirality : 0.044 0.136 1326 Planarity : 0.004 0.075 1437 Dihedral : 4.160 19.973 1185 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.81 % Favored : 93.01 % Rotamer: Outliers : 1.65 % Allowed : 30.99 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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 (0.25), residues: 1087 helix: -1.48 (0.59), residues: 73 sheet: -0.89 (0.29), residues: 391 loop : -1.89 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 198 TYR 0.008 0.001 TYR A 460 PHE 0.022 0.001 PHE A 528 TRP 0.028 0.002 TRP A 36 HIS 0.002 0.000 HIS B1077 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8207) covalent geometry : angle 0.56705 (11173) hydrogen bonds : bond 0.02726 ( 234) hydrogen bonds : angle 5.16460 ( 618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.71 seconds wall clock time: 39 minutes 33.56 seconds (2373.56 seconds total)