Starting phenix.real_space_refine on Wed Mar 4 03:37:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zn7_14802/03_2026/7zn7_14802.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zn7_14802/03_2026/7zn7_14802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zn7_14802/03_2026/7zn7_14802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zn7_14802/03_2026/7zn7_14802.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zn7_14802/03_2026/7zn7_14802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zn7_14802/03_2026/7zn7_14802.map" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.077 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 60 5.16 5 C 6666 2.51 5 N 1816 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10497 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6179 Classifications: {'peptide': 783} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 757} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3272 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 6 Chain: "D" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1045 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain breaks: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7478 SG CYS B 273 73.309 55.878 76.555 1.00 78.49 S ATOM 7492 SG CYS B 275 75.102 59.106 76.694 1.00 78.70 S ATOM 7516 SG CYS B 278 71.621 59.190 75.474 1.00 73.68 S Time building chain proxies: 2.25, per 1000 atoms: 0.21 Number of scatterers: 10497 At special positions: 0 Unit cell: (100, 125, 128.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 60 16.00 O 1954 8.00 N 1816 7.00 C 6666 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: 0.71 Conformation dependent library (CDL) restraints added in 496.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 332 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 273 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 275 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 278 " Number of angles added : 3 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2470 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 18 sheets defined 37.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1062 Processing helix chain 'A' and resid 1064 through 1068 removed outlier: 4.137A pdb=" N ILE A1068 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1090 through 1095 Processing helix chain 'A' and resid 1096 through 1100 removed outlier: 3.700A pdb=" N ILE A1100 " --> pdb=" O PHE A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.634A pdb=" N ARG A1138 " --> pdb=" O GLU A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1140 No H-bonds generated for 'chain 'A' and resid 1139 through 1140' Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.726A pdb=" N THR B 109 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.507A pdb=" N ALA B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 166 through 185 Processing helix chain 'B' and resid 193 through 215 Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.808A pdb=" N CYS B 252 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 273 removed outlier: 3.614A pdb=" N SER B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 294 removed outlier: 3.713A pdb=" N ARG B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 286 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.966A pdb=" N GLY B 323 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.509A pdb=" N MET B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.949A pdb=" N SER B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 437 removed outlier: 3.522A pdb=" N ALA B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP B 429 " --> pdb=" O GLU B 425 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 430 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 485 through 499 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 506 through 519 Processing helix chain 'B' and resid 553 through 560 Processing helix chain 'B' and resid 564 through 570 removed outlier: 3.590A pdb=" N ILE B 568 " --> pdb=" O THR B 564 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 570 " --> pdb=" O ASN B 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 176 removed outlier: 4.039A pdb=" N ILE D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 231 Processing helix chain 'D' and resid 260 through 285 Processing helix chain 'D' and resid 294 through 317 removed outlier: 4.112A pdb=" N ARG D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.515A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A1031 " --> pdb=" O VAL A1006 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 21 removed outlier: 3.875A pdb=" N GLY A 17 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 19 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 39 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU A 54 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE A 41 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.792A pdb=" N GLU A 65 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU A 90 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR A 102 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS A 92 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE A 100 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.521A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 201 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 221 Processing sheet with id=AA7, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.685A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 279 through 288 removed outlier: 6.996A pdb=" N LEU A 280 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU A 304 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N MET A 282 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL A 302 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 284 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 300 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU A 286 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.914A pdb=" N GLY A 325 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 314 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A 323 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TYR A 316 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A 321 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 359 through 365 removed outlier: 4.373A pdb=" N ASP A 361 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 363 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.636A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.636A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 739 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 793 " --> pdb=" O HIS A 803 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 811 through 820 removed outlier: 5.260A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 815 " --> pdb=" O GLY A 832 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR A 827 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR A 853 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY A 846 " --> pdb=" O GLU A 865 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU A 865 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 848 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU A 863 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 850 " --> pdb=" O VAL A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 870 through 876 removed outlier: 4.434A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 913 through 917 removed outlier: 7.031A pdb=" N VAL A 930 " --> pdb=" O ARG A 947 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG A 947 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 945 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 954 through 961 removed outlier: 6.880A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE A 959 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASN A 964 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1076 through 1077 494 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2021 1.32 - 1.45: 2533 1.45 - 1.57: 6024 1.57 - 1.69: 0 1.69 - 1.82: 92 Bond restraints: 10670 Sorted by residual: bond pdb=" N ARG B 211 " pdb=" CA ARG B 211 " ideal model delta sigma weight residual 1.459 1.410 0.049 1.21e-02 6.83e+03 1.64e+01 bond pdb=" CA ASP B 210 " pdb=" C ASP B 210 " ideal model delta sigma weight residual 1.524 1.471 0.052 1.29e-02 6.01e+03 1.63e+01 bond pdb=" CA LEU B 215 " pdb=" C LEU B 215 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.28e-02 6.10e+03 1.56e+01 bond pdb=" CA LYS D 167 " pdb=" C LYS D 167 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.35e-02 5.49e+03 1.31e+01 bond pdb=" CA ASP B 207 " pdb=" C ASP B 207 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.35e-02 5.49e+03 9.54e+00 ... (remaining 10665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 13806 2.34 - 4.68: 486 4.68 - 7.02: 83 7.02 - 9.36: 23 9.36 - 11.70: 5 Bond angle restraints: 14403 Sorted by residual: angle pdb=" N ARG D 176 " pdb=" CA ARG D 176 " pdb=" C ARG D 176 " ideal model delta sigma weight residual 113.01 103.22 9.79 1.20e+00 6.94e-01 6.65e+01 angle pdb=" N PHE D 175 " pdb=" CA PHE D 175 " pdb=" C PHE D 175 " ideal model delta sigma weight residual 113.50 103.82 9.68 1.23e+00 6.61e-01 6.19e+01 angle pdb=" N VAL B 220 " pdb=" CA VAL B 220 " pdb=" C VAL B 220 " ideal model delta sigma weight residual 108.93 100.58 8.35 1.35e+00 5.49e-01 3.83e+01 angle pdb=" N GLY A 205 " pdb=" CA GLY A 205 " pdb=" C GLY A 205 " ideal model delta sigma weight residual 112.23 119.23 -7.00 1.21e+00 6.83e-01 3.35e+01 angle pdb=" N GLY A 373 " pdb=" CA GLY A 373 " pdb=" C GLY A 373 " ideal model delta sigma weight residual 112.33 118.36 -6.03 1.10e+00 8.26e-01 3.01e+01 ... (remaining 14398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 5864 16.65 - 33.29: 481 33.29 - 49.94: 107 49.94 - 66.58: 18 66.58 - 83.23: 6 Dihedral angle restraints: 6476 sinusoidal: 2664 harmonic: 3812 Sorted by residual: dihedral pdb=" CA LEU D 287 " pdb=" C LEU D 287 " pdb=" N ARG D 288 " pdb=" CA ARG D 288 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA LYS A 74 " pdb=" C LYS A 74 " pdb=" N ASP A 75 " pdb=" CA ASP A 75 " ideal model delta harmonic sigma weight residual 180.00 155.78 24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ASN B 566 " pdb=" C ASN B 566 " pdb=" N GLU B 567 " pdb=" CA GLU B 567 " ideal model delta harmonic sigma weight residual 180.00 156.86 23.14 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 6473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1460 0.091 - 0.182: 166 0.182 - 0.274: 9 0.274 - 0.365: 3 0.365 - 0.456: 2 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CB VAL B 561 " pdb=" CA VAL B 561 " pdb=" CG1 VAL B 561 " pdb=" CG2 VAL B 561 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" CG LEU A 305 " pdb=" CB LEU A 305 " pdb=" CD1 LEU A 305 " pdb=" CD2 LEU A 305 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CG LEU A 814 " pdb=" CB LEU A 814 " pdb=" CD1 LEU A 814 " pdb=" CD2 LEU A 814 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 1637 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 965 " -0.034 2.00e-02 2.50e+03 3.90e-02 2.67e+01 pdb=" CG PHE A 965 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE A 965 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 965 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE A 965 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 965 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 965 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 145 " 0.027 2.00e-02 2.50e+03 3.62e-02 2.30e+01 pdb=" CG PHE B 145 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE B 145 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE B 145 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 145 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE B 145 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B 145 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.077 5.00e-02 4.00e+02 1.14e-01 2.10e+01 pdb=" N PRO A 126 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.062 5.00e-02 4.00e+02 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1131 2.75 - 3.29: 10566 3.29 - 3.82: 16783 3.82 - 4.36: 20848 4.36 - 4.90: 34040 Nonbonded interactions: 83368 Sorted by model distance: nonbonded pdb=" OE1 GLN A 727 " pdb=" OG1 THR A 827 " model vdw 2.209 3.040 nonbonded pdb=" OG SER A 326 " pdb=" O GLY A 329 " model vdw 2.229 3.040 nonbonded pdb=" OE1 GLU A 40 " pdb=" OH TYR A 42 " model vdw 2.246 3.040 nonbonded pdb=" NE2 GLN A 183 " pdb=" O ASP A 184 " model vdw 2.286 3.120 nonbonded pdb=" OG1 THR A 45 " pdb=" O GLY A 48 " model vdw 2.311 3.040 ... (remaining 83363 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.920 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.180 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.007 0.176 10674 Z= 0.380 Angle : 1.058 14.575 14406 Z= 0.639 Chirality : 0.058 0.456 1640 Planarity : 0.006 0.114 1852 Dihedral : 13.003 83.227 4006 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 1.39 % Allowed : 2.95 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -2.48 (0.21), residues: 1275 helix: -1.37 (0.20), residues: 444 sheet: -2.11 (0.28), residues: 299 loop : -1.37 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 150 TYR 0.038 0.003 TYR A 718 PHE 0.088 0.004 PHE A 965 TRP 0.047 0.003 TRP B 128 HIS 0.021 0.003 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00622 (10670) covalent geometry : angle 1.04559 (14403) hydrogen bonds : bond 0.22390 ( 491) hydrogen bonds : angle 9.04048 ( 1365) metal coordination : bond 0.10926 ( 4) metal coordination : angle 11.35261 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8038 (t0) REVERT: A 892 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7842 (pp20) REVERT: B 155 LEU cc_start: 0.9219 (tp) cc_final: 0.9018 (tp) REVERT: B 190 ARG cc_start: 0.7410 (mtt90) cc_final: 0.7159 (mtt90) REVERT: B 354 GLN cc_start: 0.8099 (tt0) cc_final: 0.7576 (tt0) REVERT: D 273 LEU cc_start: 0.9328 (mt) cc_final: 0.9121 (mp) outliers start: 16 outliers final: 6 residues processed: 233 average time/residue: 0.1176 time to fit residues: 37.8018 Evaluate side-chains 157 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 892 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 159 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.0170 chunk 129 optimal weight: 5.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN A 203 ASN A 262 ASN A 727 GLN A 790 ASN B 141 ASN B 179 GLN B 365 GLN B 407 HIS B 508 HIS D 170 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.176717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153255 restraints weight = 14912.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.151556 restraints weight = 24855.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.149949 restraints weight = 25286.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.147025 restraints weight = 17571.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147482 restraints weight = 18683.757| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10674 Z= 0.147 Angle : 0.655 8.589 14406 Z= 0.339 Chirality : 0.044 0.169 1640 Planarity : 0.005 0.070 1852 Dihedral : 5.588 50.932 1451 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.17 % Allowed : 10.14 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.08 (0.23), residues: 1275 helix: 0.71 (0.23), residues: 430 sheet: -1.57 (0.29), residues: 312 loop : -1.25 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 111 TYR 0.025 0.002 TYR B 386 PHE 0.023 0.002 PHE A1097 TRP 0.020 0.002 TRP A 207 HIS 0.006 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00318 (10670) covalent geometry : angle 0.65455 (14403) hydrogen bonds : bond 0.05371 ( 491) hydrogen bonds : angle 6.12818 ( 1365) metal coordination : bond 0.00471 ( 4) metal coordination : angle 1.81101 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8039 (tt) REVERT: A 262 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7954 (t0) REVERT: A 725 CYS cc_start: 0.7665 (t) cc_final: 0.7323 (m) REVERT: A 790 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8168 (p0) REVERT: A 818 SER cc_start: 0.8284 (t) cc_final: 0.8031 (p) REVERT: B 227 ASP cc_start: 0.6396 (OUTLIER) cc_final: 0.5913 (m-30) REVERT: B 315 ILE cc_start: 0.8769 (tp) cc_final: 0.8470 (tt) REVERT: D 171 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7847 (t0) outliers start: 25 outliers final: 12 residues processed: 187 average time/residue: 0.1074 time to fit residues: 28.2814 Evaluate side-chains 159 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 171 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN A 759 GLN A 789 HIS D 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.175359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151826 restraints weight = 15000.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150357 restraints weight = 27928.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151357 restraints weight = 25996.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.150872 restraints weight = 18271.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151402 restraints weight = 16238.030| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10674 Z= 0.140 Angle : 0.615 9.203 14406 Z= 0.314 Chirality : 0.043 0.185 1640 Planarity : 0.004 0.064 1852 Dihedral : 5.159 53.571 1446 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.43 % Allowed : 12.39 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.70 (0.23), residues: 1275 helix: 1.25 (0.24), residues: 430 sheet: -1.30 (0.29), residues: 331 loop : -1.29 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 288 TYR 0.018 0.002 TYR B 114 PHE 0.016 0.002 PHE A 180 TRP 0.017 0.002 TRP B 123 HIS 0.004 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00318 (10670) covalent geometry : angle 0.61520 (14403) hydrogen bonds : bond 0.04619 ( 491) hydrogen bonds : angle 5.62076 ( 1365) metal coordination : bond 0.00454 ( 4) metal coordination : angle 0.78459 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8133 (tt) REVERT: A 262 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7964 (t0) REVERT: A 725 CYS cc_start: 0.7597 (t) cc_final: 0.7366 (m) REVERT: B 201 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7941 (mp) REVERT: B 227 ASP cc_start: 0.6054 (OUTLIER) cc_final: 0.5578 (m-30) REVERT: B 315 ILE cc_start: 0.8759 (tp) cc_final: 0.8451 (tt) REVERT: B 412 PHE cc_start: 0.8080 (m-80) cc_final: 0.7800 (m-10) outliers start: 28 outliers final: 15 residues processed: 175 average time/residue: 0.1061 time to fit residues: 26.2692 Evaluate side-chains 157 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 283 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 29 optimal weight: 0.7980 chunk 110 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN A 790 ASN B 141 ASN B 209 GLN ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.174306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150978 restraints weight = 14958.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150164 restraints weight = 26305.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151239 restraints weight = 25434.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.150678 restraints weight = 17853.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151255 restraints weight = 16290.405| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10674 Z= 0.141 Angle : 0.609 13.994 14406 Z= 0.306 Chirality : 0.042 0.181 1640 Planarity : 0.004 0.061 1852 Dihedral : 4.820 49.970 1444 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.77 % Allowed : 13.86 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.47 (0.24), residues: 1275 helix: 1.57 (0.25), residues: 431 sheet: -1.13 (0.30), residues: 330 loop : -1.32 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 509 TYR 0.023 0.002 TYR B 386 PHE 0.015 0.002 PHE D 175 TRP 0.013 0.002 TRP B 128 HIS 0.004 0.001 HIS A1077 Details of bonding type rmsd covalent geometry : bond 0.00319 (10670) covalent geometry : angle 0.60894 (14403) hydrogen bonds : bond 0.04223 ( 491) hydrogen bonds : angle 5.30800 ( 1365) metal coordination : bond 0.00722 ( 4) metal coordination : angle 0.41311 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8431 (t0) REVERT: A 246 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8118 (tt) REVERT: A 313 CYS cc_start: 0.7974 (t) cc_final: 0.6906 (p) REVERT: A 362 MET cc_start: 0.8039 (ptt) cc_final: 0.7782 (ptt) REVERT: A 790 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7996 (p0) REVERT: B 201 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7945 (mp) REVERT: B 315 ILE cc_start: 0.8796 (tp) cc_final: 0.8471 (tt) outliers start: 32 outliers final: 19 residues processed: 181 average time/residue: 0.0961 time to fit residues: 25.5012 Evaluate side-chains 162 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 283 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 125 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN ** B 332 HIS ** 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 = 0.4164 r_free = 0.4164 target = 0.174192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150658 restraints weight = 15023.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.148929 restraints weight = 25618.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.149009 restraints weight = 24781.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.147599 restraints weight = 22118.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.148134 restraints weight = 19822.079| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10674 Z= 0.133 Angle : 0.598 8.649 14406 Z= 0.303 Chirality : 0.042 0.179 1640 Planarity : 0.004 0.059 1852 Dihedral : 4.649 49.472 1442 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.86 % Allowed : 13.78 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.39 (0.24), residues: 1275 helix: 1.62 (0.24), residues: 431 sheet: -0.96 (0.30), residues: 326 loop : -1.38 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 418 TYR 0.023 0.001 TYR B 386 PHE 0.030 0.002 PHE A1097 TRP 0.015 0.002 TRP B 128 HIS 0.004 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00303 (10670) covalent geometry : angle 0.59753 (14403) hydrogen bonds : bond 0.04048 ( 491) hydrogen bonds : angle 5.21365 ( 1365) metal coordination : bond 0.00750 ( 4) metal coordination : angle 0.44389 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8166 (tt) REVERT: B 232 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.6958 (mp10) REVERT: B 315 ILE cc_start: 0.8783 (tp) cc_final: 0.8477 (tt) REVERT: D 175 PHE cc_start: 0.7216 (t80) cc_final: 0.6845 (t80) outliers start: 33 outliers final: 17 residues processed: 172 average time/residue: 0.0976 time to fit residues: 24.5180 Evaluate side-chains 159 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 283 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 34 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS A 790 ASN B 141 ASN B 209 GLN ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.170951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147233 restraints weight = 15089.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145467 restraints weight = 27523.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146659 restraints weight = 27477.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145554 restraints weight = 19286.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146340 restraints weight = 19370.234| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10674 Z= 0.185 Angle : 0.635 10.644 14406 Z= 0.325 Chirality : 0.044 0.242 1640 Planarity : 0.004 0.059 1852 Dihedral : 4.760 50.420 1442 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.12 % Allowed : 15.42 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.41 (0.24), residues: 1275 helix: 1.79 (0.24), residues: 430 sheet: -1.08 (0.30), residues: 329 loop : -1.46 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 157 TYR 0.014 0.002 TYR A 42 PHE 0.017 0.002 PHE A 851 TRP 0.028 0.002 TRP B 123 HIS 0.005 0.001 HIS A1077 Details of bonding type rmsd covalent geometry : bond 0.00439 (10670) covalent geometry : angle 0.63504 (14403) hydrogen bonds : bond 0.04182 ( 491) hydrogen bonds : angle 5.16043 ( 1365) metal coordination : bond 0.01576 ( 4) metal coordination : angle 0.48854 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8034 (tt) REVERT: A 313 CYS cc_start: 0.7784 (t) cc_final: 0.6858 (p) REVERT: A 790 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7852 (p0) REVERT: B 232 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: B 315 ILE cc_start: 0.8786 (tp) cc_final: 0.8484 (tt) outliers start: 36 outliers final: 20 residues processed: 172 average time/residue: 0.1053 time to fit residues: 25.9063 Evaluate side-chains 159 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 283 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 48 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** 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 = 0.4148 r_free = 0.4148 target = 0.172516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.148797 restraints weight = 14925.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147165 restraints weight = 26518.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.147971 restraints weight = 27057.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147632 restraints weight = 18471.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.148177 restraints weight = 17727.436| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10674 Z= 0.138 Angle : 0.617 9.438 14406 Z= 0.312 Chirality : 0.043 0.204 1640 Planarity : 0.004 0.059 1852 Dihedral : 4.592 49.445 1440 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.34 % Allowed : 16.55 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.42 (0.24), residues: 1275 helix: 1.75 (0.24), residues: 430 sheet: -1.08 (0.30), residues: 331 loop : -1.46 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 900 TYR 0.016 0.001 TYR A 906 PHE 0.034 0.002 PHE A1097 TRP 0.018 0.002 TRP A 953 HIS 0.005 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00320 (10670) covalent geometry : angle 0.61720 (14403) hydrogen bonds : bond 0.04022 ( 491) hydrogen bonds : angle 5.14261 ( 1365) metal coordination : bond 0.01006 ( 4) metal coordination : angle 0.35956 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8058 (tt) REVERT: A 313 CYS cc_start: 0.7647 (t) cc_final: 0.6798 (p) REVERT: A 1097 PHE cc_start: 0.7431 (t80) cc_final: 0.7230 (t80) REVERT: A 1105 MET cc_start: 0.6763 (mmm) cc_final: 0.6491 (mmm) REVERT: B 205 TYR cc_start: 0.8110 (t80) cc_final: 0.7792 (t80) REVERT: B 209 GLN cc_start: 0.7409 (mt0) cc_final: 0.6848 (mt0) REVERT: B 232 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.6959 (mp10) REVERT: B 315 ILE cc_start: 0.8757 (tp) cc_final: 0.8447 (tt) outliers start: 27 outliers final: 17 residues processed: 167 average time/residue: 0.0959 time to fit residues: 23.5380 Evaluate side-chains 161 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 283 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 113 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 241 ASN A 790 ASN A 908 ASN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 209 GLN ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.165034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141406 restraints weight = 15199.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139812 restraints weight = 28093.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140973 restraints weight = 28250.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140574 restraints weight = 18629.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.141049 restraints weight = 20629.493| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 10674 Z= 0.318 Angle : 0.778 9.082 14406 Z= 0.400 Chirality : 0.048 0.220 1640 Planarity : 0.005 0.055 1852 Dihedral : 5.187 51.763 1440 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.95 % Allowed : 17.24 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.79 (0.24), residues: 1275 helix: 1.55 (0.24), residues: 437 sheet: -1.58 (0.29), residues: 308 loop : -1.61 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 900 TYR 0.026 0.003 TYR A 346 PHE 0.031 0.003 PHE A1097 TRP 0.021 0.003 TRP A 953 HIS 0.008 0.002 HIS A1077 Details of bonding type rmsd covalent geometry : bond 0.00768 (10670) covalent geometry : angle 0.77793 (14403) hydrogen bonds : bond 0.04792 ( 491) hydrogen bonds : angle 5.49386 ( 1365) metal coordination : bond 0.02868 ( 4) metal coordination : angle 1.70090 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.7977 (m110) cc_final: 0.7776 (m-40) REVERT: A 246 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8198 (tt) REVERT: A 790 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8248 (p0) REVERT: A 910 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.5421 (ptp) REVERT: A 932 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8501 (tt) REVERT: A 1097 PHE cc_start: 0.7888 (t80) cc_final: 0.7497 (t80) REVERT: A 1105 MET cc_start: 0.7146 (mmm) cc_final: 0.6809 (mmm) REVERT: B 232 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7059 (mp10) outliers start: 34 outliers final: 20 residues processed: 153 average time/residue: 0.1055 time to fit residues: 23.0665 Evaluate side-chains 150 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 283 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 96 optimal weight: 0.0370 chunk 102 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 124 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 267 ASN A 790 ASN B 141 ASN B 209 GLN ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.171377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.148199 restraints weight = 14929.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.146746 restraints weight = 25887.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145049 restraints weight = 26515.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.142107 restraints weight = 21819.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142779 restraints weight = 21076.964| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10674 Z= 0.129 Angle : 0.663 13.160 14406 Z= 0.330 Chirality : 0.045 0.330 1640 Planarity : 0.004 0.059 1852 Dihedral : 4.755 47.443 1440 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.08 % Allowed : 18.11 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.59 (0.24), residues: 1275 helix: 1.59 (0.24), residues: 441 sheet: -1.27 (0.30), residues: 307 loop : -1.55 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 900 TYR 0.028 0.001 TYR B 205 PHE 0.030 0.002 PHE A1097 TRP 0.022 0.003 TRP B 128 HIS 0.006 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00288 (10670) covalent geometry : angle 0.66279 (14403) hydrogen bonds : bond 0.04052 ( 491) hydrogen bonds : angle 5.22620 ( 1365) metal coordination : bond 0.01026 ( 4) metal coordination : angle 0.90180 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7426 (mmp) cc_final: 0.7070 (mmt) REVERT: A 246 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8041 (tt) REVERT: A 313 CYS cc_start: 0.7393 (t) cc_final: 0.6633 (p) REVERT: A 790 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8354 (p0) REVERT: A 1097 PHE cc_start: 0.7630 (t80) cc_final: 0.7416 (t80) REVERT: A 1105 MET cc_start: 0.7248 (mmm) cc_final: 0.6885 (mmm) REVERT: B 232 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.6890 (mp10) REVERT: B 315 ILE cc_start: 0.8773 (tp) cc_final: 0.8465 (tt) outliers start: 24 outliers final: 16 residues processed: 154 average time/residue: 0.1003 time to fit residues: 22.5776 Evaluate side-chains 151 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 283 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 119 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.167574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144387 restraints weight = 14976.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.142999 restraints weight = 25611.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141378 restraints weight = 26028.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138524 restraints weight = 18035.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139009 restraints weight = 19758.389| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10674 Z= 0.222 Angle : 0.689 11.782 14406 Z= 0.350 Chirality : 0.045 0.201 1640 Planarity : 0.004 0.059 1852 Dihedral : 4.855 49.757 1440 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.99 % Allowed : 18.02 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.73 (0.24), residues: 1275 helix: 1.60 (0.24), residues: 439 sheet: -1.45 (0.29), residues: 328 loop : -1.65 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 722 TYR 0.023 0.002 TYR B 205 PHE 0.028 0.002 PHE A1097 TRP 0.021 0.002 TRP B 128 HIS 0.006 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00537 (10670) covalent geometry : angle 0.68931 (14403) hydrogen bonds : bond 0.04222 ( 491) hydrogen bonds : angle 5.24650 ( 1365) metal coordination : bond 0.01887 ( 4) metal coordination : angle 0.80187 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7610 (mmp) cc_final: 0.7276 (mmt) REVERT: A 246 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8163 (tt) REVERT: A 313 CYS cc_start: 0.7482 (t) cc_final: 0.6502 (p) REVERT: A 790 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8399 (p0) REVERT: A 932 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 1097 PHE cc_start: 0.7764 (t80) cc_final: 0.7459 (t80) REVERT: A 1105 MET cc_start: 0.7706 (mmm) cc_final: 0.7244 (mmm) REVERT: B 232 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.6911 (mp10) outliers start: 23 outliers final: 17 residues processed: 153 average time/residue: 0.0952 time to fit residues: 20.9383 Evaluate side-chains 149 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 283 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN B 141 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.170165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.146439 restraints weight = 14990.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145104 restraints weight = 26358.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145828 restraints weight = 26638.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.143379 restraints weight = 20477.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144141 restraints weight = 19713.959| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10674 Z= 0.140 Angle : 0.649 11.670 14406 Z= 0.326 Chirality : 0.044 0.272 1640 Planarity : 0.004 0.059 1852 Dihedral : 4.714 48.418 1440 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.99 % Allowed : 18.37 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.61 (0.24), residues: 1275 helix: 1.68 (0.24), residues: 434 sheet: -1.25 (0.31), residues: 302 loop : -1.64 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.027 0.002 TYR A 182 PHE 0.029 0.002 PHE A1097 TRP 0.023 0.002 TRP B 128 HIS 0.006 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00328 (10670) covalent geometry : angle 0.64922 (14403) hydrogen bonds : bond 0.03983 ( 491) hydrogen bonds : angle 5.16921 ( 1365) metal coordination : bond 0.01050 ( 4) metal coordination : angle 0.69546 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1621.10 seconds wall clock time: 28 minutes 54.86 seconds (1734.86 seconds total)