Starting phenix.real_space_refine on Mon Jul 28 17:35:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zn7_14802/07_2025/7zn7_14802.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zn7_14802/07_2025/7zn7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zn7_14802/07_2025/7zn7_14802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zn7_14802/07_2025/7zn7_14802.map" model { file = "/net/cci-nas-00/data/ceres_data/7zn7_14802/07_2025/7zn7_14802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zn7_14802/07_2025/7zn7_14802.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.71, per 1000 atoms: 0.73 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: 2.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.48 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: 4.80 Time building geometry restraints manager: 3.05 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.280 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.047 0.003 TRP B 128 HIS 0.021 0.003 HIS D 272 PHE 0.088 0.004 PHE A 965 TYR 0.038 0.003 TYR A 718 ARG 0.005 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.22390 ( 491) hydrogen bonds : angle 9.04048 ( 1365) metal coordination : bond 0.10926 ( 4) metal coordination : angle 11.35261 ( 3) covalent geometry : bond 0.00622 (10670) covalent geometry : angle 1.04559 (14403) *********************** 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 : 1.263 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: 0.7158 (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: 0.2455 time to fit residues: 78.6441 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 : 1.115 ------------------------------------------------------------------------------- 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 109 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.175213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.151794 restraints weight = 14799.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150823 restraints weight = 26517.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.151686 restraints weight = 25676.395| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10674 Z= 0.161 Angle : 0.663 8.476 14406 Z= 0.345 Chirality : 0.044 0.163 1640 Planarity : 0.005 0.068 1852 Dihedral : 5.622 51.164 1451 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.43 % Allowed : 9.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.23), residues: 1275 helix: 0.63 (0.23), residues: 437 sheet: -1.58 (0.29), residues: 310 loop : -1.34 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 207 HIS 0.005 0.001 HIS B 407 PHE 0.023 0.002 PHE A1097 TYR 0.023 0.002 TYR B 386 ARG 0.007 0.000 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.05571 ( 491) hydrogen bonds : angle 6.16642 ( 1365) metal coordination : bond 0.00754 ( 4) metal coordination : angle 1.91238 ( 3) covalent geometry : bond 0.00364 (10670) covalent geometry : angle 0.66214 (14403) *********************** 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 199 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8084 (tt) REVERT: A 262 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7907 (t0) REVERT: A 725 CYS cc_start: 0.7668 (t) cc_final: 0.7306 (m) REVERT: A 818 SER cc_start: 0.8329 (t) cc_final: 0.8062 (p) REVERT: B 315 ILE cc_start: 0.8720 (tp) cc_final: 0.8403 (tt) outliers start: 28 outliers final: 18 residues processed: 188 average time/residue: 0.3018 time to fit residues: 79.6637 Evaluate side-chains 161 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 152 LEU 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 A residue 1094 ILE 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 D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 789 HIS ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.169241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.146322 restraints weight = 15144.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.145510 restraints weight = 27296.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.146039 restraints weight = 27262.921| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 10674 Z= 0.249 Angle : 0.696 10.974 14406 Z= 0.360 Chirality : 0.045 0.184 1640 Planarity : 0.004 0.063 1852 Dihedral : 5.636 58.367 1448 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.95 % Allowed : 12.31 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1275 helix: 1.26 (0.24), residues: 429 sheet: -1.57 (0.29), residues: 323 loop : -1.37 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 123 HIS 0.008 0.002 HIS A 999 PHE 0.022 0.002 PHE A 975 TYR 0.019 0.002 TYR A 42 ARG 0.005 0.001 ARG B 465 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 491) hydrogen bonds : angle 5.76200 ( 1365) metal coordination : bond 0.02109 ( 4) metal coordination : angle 0.80852 ( 3) covalent geometry : bond 0.00596 (10670) covalent geometry : angle 0.69622 (14403) *********************** 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 181 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8350 (t0) REVERT: A 246 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8184 (tt) REVERT: A 313 CYS cc_start: 0.7904 (t) cc_final: 0.6903 (p) REVERT: A 1097 PHE cc_start: 0.7619 (t80) cc_final: 0.7218 (t80) REVERT: A 1105 MET cc_start: 0.6477 (mtm) cc_final: 0.6191 (mmm) REVERT: B 315 ILE cc_start: 0.8842 (tp) cc_final: 0.8527 (tt) outliers start: 34 outliers final: 22 residues processed: 169 average time/residue: 0.3180 time to fit residues: 78.1457 Evaluate side-chains 156 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 125 ASP 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 932 LEU Chi-restraints excluded: chain A residue 1094 ILE 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 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 159 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.0370 chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 112 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 240 HIS A 790 ASN B 141 ASN ** 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 = 0.4150 r_free = 0.4150 target = 0.172755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.149476 restraints weight = 14829.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147634 restraints weight = 25441.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.148311 restraints weight = 25060.018| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10674 Z= 0.127 Angle : 0.599 9.768 14406 Z= 0.305 Chirality : 0.042 0.180 1640 Planarity : 0.004 0.060 1852 Dihedral : 5.316 58.290 1446 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.95 % Allowed : 13.43 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.24), residues: 1275 helix: 1.58 (0.24), residues: 431 sheet: -1.27 (0.30), residues: 330 loop : -1.46 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 123 HIS 0.004 0.001 HIS D 272 PHE 0.016 0.002 PHE D 175 TYR 0.019 0.001 TYR B 114 ARG 0.003 0.000 ARG A 900 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 491) hydrogen bonds : angle 5.39972 ( 1365) metal coordination : bond 0.00739 ( 4) metal coordination : angle 0.28423 ( 3) covalent geometry : bond 0.00288 (10670) covalent geometry : angle 0.59903 (14403) *********************** 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 194 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8692 (t0) REVERT: A 246 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8092 (tt) REVERT: A 313 CYS cc_start: 0.7494 (t) cc_final: 0.6811 (p) REVERT: A 1097 PHE cc_start: 0.7510 (t80) cc_final: 0.6954 (t80) REVERT: A 1105 MET cc_start: 0.6149 (mtm) cc_final: 0.5927 (mmm) REVERT: B 227 ASP cc_start: 0.6000 (OUTLIER) cc_final: 0.5531 (m-30) REVERT: B 315 ILE cc_start: 0.8719 (tp) cc_final: 0.8402 (tt) REVERT: D 175 PHE cc_start: 0.7177 (t80) cc_final: 0.6845 (t80) outliers start: 34 outliers final: 20 residues processed: 181 average time/residue: 0.3151 time to fit residues: 84.1126 Evaluate side-chains 165 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 162 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 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 B residue 116 ILE Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 194 VAL 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 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 275 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 94 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 31 optimal weight: 0.0050 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 HIS D 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.171124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.148099 restraints weight = 14950.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146760 restraints weight = 25283.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147797 restraints weight = 24437.870| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10674 Z= 0.160 Angle : 0.610 9.340 14406 Z= 0.313 Chirality : 0.043 0.183 1640 Planarity : 0.004 0.058 1852 Dihedral : 5.329 59.213 1446 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.77 % Allowed : 14.38 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1275 helix: 1.73 (0.25), residues: 436 sheet: -1.24 (0.29), residues: 334 loop : -1.40 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 123 HIS 0.005 0.001 HIS D 272 PHE 0.018 0.002 PHE A 851 TYR 0.023 0.002 TYR B 386 ARG 0.003 0.000 ARG A 722 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 491) hydrogen bonds : angle 5.28973 ( 1365) metal coordination : bond 0.01137 ( 4) metal coordination : angle 0.21417 ( 3) covalent geometry : bond 0.00374 (10670) covalent geometry : angle 0.60963 (14403) *********************** 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 188 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8241 (t0) REVERT: A 246 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8139 (tt) REVERT: A 313 CYS cc_start: 0.7662 (t) cc_final: 0.6739 (p) REVERT: A 1097 PHE cc_start: 0.7574 (t80) cc_final: 0.6999 (t80) REVERT: A 1105 MET cc_start: 0.6240 (mtm) cc_final: 0.5993 (mmm) REVERT: B 232 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: B 315 ILE cc_start: 0.8727 (tp) cc_final: 0.8411 (tt) REVERT: D 175 PHE cc_start: 0.7339 (t80) cc_final: 0.6981 (t80) outliers start: 32 outliers final: 22 residues processed: 175 average time/residue: 0.3137 time to fit residues: 77.9278 Evaluate side-chains 167 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 85 ASN 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 366 ASP 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 1052 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 194 VAL 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 485 PHE Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 275 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 94 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 186 GLN A 241 ASN A 267 ASN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 332 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 = 0.4106 r_free = 0.4106 target = 0.168812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145377 restraints weight = 15096.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144402 restraints weight = 26412.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.144752 restraints weight = 26451.219| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10674 Z= 0.201 Angle : 0.648 10.207 14406 Z= 0.330 Chirality : 0.044 0.164 1640 Planarity : 0.004 0.056 1852 Dihedral : 5.300 58.962 1444 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.03 % Allowed : 15.08 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1275 helix: 1.73 (0.25), residues: 435 sheet: -1.38 (0.29), residues: 322 loop : -1.38 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 128 HIS 0.005 0.001 HIS A1077 PHE 0.019 0.002 PHE A 851 TYR 0.022 0.002 TYR B 386 ARG 0.005 0.000 ARG D 274 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 491) hydrogen bonds : angle 5.28569 ( 1365) metal coordination : bond 0.01794 ( 4) metal coordination : angle 0.40828 ( 3) covalent geometry : bond 0.00483 (10670) covalent geometry : angle 0.64761 (14403) *********************** 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 181 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8169 (tt) REVERT: A 313 CYS cc_start: 0.7509 (t) cc_final: 0.6799 (p) REVERT: A 1105 MET cc_start: 0.6280 (mtm) cc_final: 0.5960 (mmm) REVERT: B 201 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 232 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7006 (mp10) REVERT: B 315 ILE cc_start: 0.8792 (tp) cc_final: 0.8466 (tt) REVERT: D 175 PHE cc_start: 0.7553 (t80) cc_final: 0.7193 (t80) outliers start: 35 outliers final: 23 residues processed: 170 average time/residue: 0.2198 time to fit residues: 53.6456 Evaluate side-chains 167 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 197 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1036 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 194 VAL 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 485 PHE Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 275 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 44 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4092 r_free = 0.4092 target = 0.167427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.143943 restraints weight = 15247.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.142846 restraints weight = 27502.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.143670 restraints weight = 26929.311| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 10674 Z= 0.239 Angle : 0.681 8.852 14406 Z= 0.348 Chirality : 0.045 0.198 1640 Planarity : 0.004 0.057 1852 Dihedral : 5.378 58.361 1444 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.21 % Allowed : 16.12 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1275 helix: 1.69 (0.24), residues: 437 sheet: -1.52 (0.28), residues: 330 loop : -1.47 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 128 HIS 0.006 0.001 HIS A 999 PHE 0.020 0.002 PHE D 175 TYR 0.022 0.002 TYR B 386 ARG 0.006 0.000 ARG A 900 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 491) hydrogen bonds : angle 5.33654 ( 1365) metal coordination : bond 0.02139 ( 4) metal coordination : angle 0.73447 ( 3) covalent geometry : bond 0.00576 (10670) covalent geometry : angle 0.68109 (14403) *********************** 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 175 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8180 (tt) REVERT: A 313 CYS cc_start: 0.7657 (t) cc_final: 0.6794 (p) REVERT: A 1105 MET cc_start: 0.6341 (mtm) cc_final: 0.5982 (mmm) REVERT: B 201 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7931 (mp) REVERT: B 232 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: B 315 ILE cc_start: 0.8835 (tp) cc_final: 0.8527 (tt) REVERT: D 175 PHE cc_start: 0.7837 (t80) cc_final: 0.7479 (t80) outliers start: 37 outliers final: 24 residues processed: 165 average time/residue: 0.3405 time to fit residues: 80.9042 Evaluate side-chains 160 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 THR 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 238 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 194 VAL 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 350 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 485 PHE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 275 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 103 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 125 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN A 186 GLN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** 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 = 0.4128 r_free = 0.4128 target = 0.170669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.147454 restraints weight = 14931.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146482 restraints weight = 25152.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147079 restraints weight = 26702.354| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3779 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= 0.143 Angle : 0.641 13.586 14406 Z= 0.316 Chirality : 0.043 0.247 1640 Planarity : 0.004 0.058 1852 Dihedral : 5.160 57.564 1444 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.91 % Allowed : 17.68 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1275 helix: 1.73 (0.24), residues: 437 sheet: -1.24 (0.30), residues: 315 loop : -1.47 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 128 HIS 0.006 0.001 HIS D 272 PHE 0.018 0.001 PHE D 175 TYR 0.016 0.001 TYR B 114 ARG 0.004 0.000 ARG A 900 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 491) hydrogen bonds : angle 5.16798 ( 1365) metal coordination : bond 0.01039 ( 4) metal coordination : angle 0.70317 ( 3) covalent geometry : bond 0.00333 (10670) covalent geometry : angle 0.64064 (14403) *********************** 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 176 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8096 (tt) REVERT: A 313 CYS cc_start: 0.7436 (t) cc_final: 0.6780 (p) REVERT: A 1105 MET cc_start: 0.6242 (mtm) cc_final: 0.5902 (mmm) REVERT: B 201 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8012 (mp) REVERT: B 232 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: B 315 ILE cc_start: 0.8719 (tp) cc_final: 0.8384 (tt) REVERT: D 175 PHE cc_start: 0.7745 (t80) cc_final: 0.7351 (t80) outliers start: 22 outliers final: 18 residues processed: 168 average time/residue: 0.3059 time to fit residues: 72.8747 Evaluate side-chains 157 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR 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 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 B residue 116 ILE Chi-restraints excluded: chain B residue 176 VAL 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 485 PHE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 212 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 128 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 125 optimal weight: 0.0070 chunk 8 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 790 ASN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 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 = 0.4131 r_free = 0.4131 target = 0.171014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147359 restraints weight = 15163.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146061 restraints weight = 27598.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.147535 restraints weight = 26666.253| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10674 Z= 0.147 Angle : 0.641 15.548 14406 Z= 0.320 Chirality : 0.043 0.182 1640 Planarity : 0.004 0.059 1852 Dihedral : 5.139 59.050 1444 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.60 % Allowed : 17.33 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1275 helix: 1.84 (0.24), residues: 428 sheet: -1.25 (0.29), residues: 339 loop : -1.48 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 128 HIS 0.006 0.001 HIS D 272 PHE 0.020 0.002 PHE D 175 TYR 0.015 0.001 TYR B 386 ARG 0.004 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 491) hydrogen bonds : angle 5.07453 ( 1365) metal coordination : bond 0.01175 ( 4) metal coordination : angle 0.58516 ( 3) covalent geometry : bond 0.00350 (10670) covalent geometry : angle 0.64090 (14403) *********************** 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 179 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8097 (tt) REVERT: A 313 CYS cc_start: 0.7494 (t) cc_final: 0.6695 (p) REVERT: A 1105 MET cc_start: 0.6424 (mtm) cc_final: 0.6035 (mmm) REVERT: B 201 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 232 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: B 315 ILE cc_start: 0.8689 (tp) cc_final: 0.8382 (tt) REVERT: D 175 PHE cc_start: 0.7896 (t80) cc_final: 0.7420 (t80) outliers start: 30 outliers final: 23 residues processed: 169 average time/residue: 0.2252 time to fit residues: 54.0181 Evaluate side-chains 163 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR 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 790 ASN Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1086 THR 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 228 MET Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 330 ILE 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 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 9 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 0.0770 chunk 95 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 790 ASN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.168513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144815 restraints weight = 15035.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143001 restraints weight = 27291.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144512 restraints weight = 27096.678| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10674 Z= 0.195 Angle : 0.687 13.546 14406 Z= 0.345 Chirality : 0.045 0.391 1640 Planarity : 0.004 0.059 1852 Dihedral : 5.252 58.505 1444 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.43 % Allowed : 18.20 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1275 helix: 1.83 (0.24), residues: 429 sheet: -1.36 (0.29), residues: 337 loop : -1.55 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 128 HIS 0.006 0.001 HIS D 272 PHE 0.021 0.002 PHE D 175 TYR 0.016 0.002 TYR B 386 ARG 0.004 0.000 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 491) hydrogen bonds : angle 5.15239 ( 1365) metal coordination : bond 0.01700 ( 4) metal coordination : angle 0.77275 ( 3) covalent geometry : bond 0.00470 (10670) covalent geometry : angle 0.68667 (14403) ********************** 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 169 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8143 (tt) REVERT: A 297 LEU cc_start: 0.8636 (tp) cc_final: 0.8068 (tp) REVERT: A 313 CYS cc_start: 0.7671 (t) cc_final: 0.6764 (p) REVERT: A 790 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8189 (p0) REVERT: A 1105 MET cc_start: 0.6505 (mtm) cc_final: 0.6080 (mmm) REVERT: B 201 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7956 (mp) REVERT: B 232 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.6950 (mp10) outliers start: 28 outliers final: 22 residues processed: 161 average time/residue: 0.2281 time to fit residues: 52.0559 Evaluate side-chains 160 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR 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 790 ASN Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 860 THR 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 A residue 1086 THR 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 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 485 PHE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 2 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 0.0070 chunk 52 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- 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 790 ASN A 908 ASN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.169114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.145225 restraints weight = 15071.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.143710 restraints weight = 27983.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144761 restraints weight = 28715.857| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10674 Z= 0.169 Angle : 0.674 13.741 14406 Z= 0.337 Chirality : 0.043 0.195 1640 Planarity : 0.004 0.059 1852 Dihedral : 5.217 59.244 1444 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.25 % Allowed : 18.02 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.24), residues: 1275 helix: 1.83 (0.25), residues: 431 sheet: -1.26 (0.30), residues: 311 loop : -1.60 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 128 HIS 0.006 0.001 HIS D 272 PHE 0.022 0.002 PHE D 175 TYR 0.015 0.002 TYR B 386 ARG 0.009 0.000 ARG B 157 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 491) hydrogen bonds : angle 5.13272 ( 1365) metal coordination : bond 0.01419 ( 4) metal coordination : angle 0.67498 ( 3) covalent geometry : bond 0.00406 (10670) covalent geometry : angle 0.67394 (14403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3568.29 seconds wall clock time: 67 minutes 7.85 seconds (4027.85 seconds total)