Starting phenix.real_space_refine on Wed Mar 4 13:06:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzw_24780/03_2026/7rzw_24780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzw_24780/03_2026/7rzw_24780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rzw_24780/03_2026/7rzw_24780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzw_24780/03_2026/7rzw_24780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rzw_24780/03_2026/7rzw_24780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzw_24780/03_2026/7rzw_24780.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 8675 2.51 5 N 2336 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13616 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6749 Classifications: {'peptide': 859} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 821} Chain breaks: 5 Chain: "B" Number of atoms: 6781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 6781 Classifications: {'peptide': 864} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 826} Chain breaks: 4 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.07, per 1000 atoms: 0.23 Number of scatterers: 13616 At special positions: 0 Unit cell: (124.509, 119.364, 113.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2500 8.00 N 2336 7.00 C 8675 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 533.6 milliseconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3226 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 18 sheets defined 41.7% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 104 through 111 removed outlier: 3.570A pdb=" N GLN A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.136A pdb=" N PHE A 167 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.527A pdb=" N VAL A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 247 removed outlier: 3.965A pdb=" N LEU A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 269 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 411 through 456 removed outlier: 3.871A pdb=" N LEU A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 removed outlier: 4.369A pdb=" N VAL A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 509 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 600 through 621 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 824 through 829 Processing helix chain 'A' and resid 835 through 840 Processing helix chain 'A' and resid 848 through 863 removed outlier: 3.900A pdb=" N LYS A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 920 removed outlier: 3.792A pdb=" N GLN A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 939 Processing helix chain 'A' and resid 939 through 954 Processing helix chain 'A' and resid 959 through 983 removed outlier: 3.722A pdb=" N GLN A 975 " --> pdb=" O SER A 971 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 976 " --> pdb=" O CYS A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1007 removed outlier: 3.573A pdb=" N ILE A1006 " --> pdb=" O LEU A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1020 removed outlier: 3.619A pdb=" N ARG A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1058 removed outlier: 3.513A pdb=" N ILE A1044 " --> pdb=" O ASP A1040 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A1054 " --> pdb=" O GLU A1050 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A1058 " --> pdb=" O SER A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 removed outlier: 3.650A pdb=" N VAL A1101 " --> pdb=" O PRO A1097 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A1102 " --> pdb=" O PRO A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1128 removed outlier: 3.644A pdb=" N LEU A1125 " --> pdb=" O CYS A1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.826A pdb=" N SER B 165 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.725A pdb=" N ILE B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.310A pdb=" N LEU B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 245 removed outlier: 3.697A pdb=" N SER B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.698A pdb=" N VAL B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'B' and resid 411 through 454 Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.593A pdb=" N GLY B 462 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 463 " --> pdb=" O PRO B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 474 removed outlier: 3.548A pdb=" N LEU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 469 through 474' Processing helix chain 'B' and resid 495 through 509 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 533 Processing helix chain 'B' and resid 600 through 620 removed outlier: 3.760A pdb=" N LYS B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 821 Processing helix chain 'B' and resid 824 through 829 Processing helix chain 'B' and resid 848 through 862 Processing helix chain 'B' and resid 908 through 953 removed outlier: 4.509A pdb=" N ASP B 922 " --> pdb=" O GLN B 918 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE B 926 " --> pdb=" O ASP B 922 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 927 " --> pdb=" O THR B 923 " (cutoff:3.500A) Proline residue: B 942 - end of helix Processing helix chain 'B' and resid 959 through 980 Processing helix chain 'B' and resid 1001 through 1021 removed outlier: 3.963A pdb=" N VAL B1005 " --> pdb=" O PHE B1001 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B1015 " --> pdb=" O SER B1011 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU B1016 " --> pdb=" O GLN B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1058 Processing helix chain 'B' and resid 1097 through 1107 removed outlier: 3.574A pdb=" N VAL B1101 " --> pdb=" O PRO B1097 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B1107 " --> pdb=" O ASP B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1128 removed outlier: 3.832A pdb=" N LEU B1125 " --> pdb=" O CYS B1121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.651A pdb=" N ARG A 129 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA A 122 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 190 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.651A pdb=" N ARG A 129 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA A 122 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 302 through 303 removed outlier: 6.227A pdb=" N VAL A 275 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A 289 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 273 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP A 397 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 375 " --> pdb=" O TRP A 397 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU A 399 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET A 373 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A 401 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 371 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS A 403 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA A 369 " --> pdb=" O HIS A 403 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 491 removed outlier: 3.573A pdb=" N ASP A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 515 " --> pdb=" O ILE A 781 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 783 " --> pdb=" O GLY A 515 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER A 517 " --> pdb=" O ILE A 783 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 560 through 564 Processing sheet with id=AA7, first strand: chain 'A' and resid 810 through 813 removed outlier: 6.290A pdb=" N ALA A 803 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TRP A 813 " --> pdb=" O ILE A 801 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE A 801 " --> pdb=" O TRP A 813 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ALA A 887 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASP A 867 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 998 through 1000 removed outlier: 3.912A pdb=" N PHE A1000 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A1037 " --> pdb=" O PHE A1000 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1023 through 1027 removed outlier: 3.703A pdb=" N VAL A1065 " --> pdb=" O GLN A1023 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A1027 " --> pdb=" O ILE A1067 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1071 through 1075 Processing sheet with id=AB2, first strand: chain 'B' and resid 113 through 114 removed outlier: 6.357A pdb=" N MET B 120 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 190 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 302 through 303 removed outlier: 5.355A pdb=" N VAL B 286 " --> pdb=" O LYS B 277 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 277 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 288 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TRP B 397 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL B 375 " --> pdb=" O TRP B 397 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 399 " --> pdb=" O MET B 373 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET B 373 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 302 through 303 removed outlier: 5.355A pdb=" N VAL B 286 " --> pdb=" O LYS B 277 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 277 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 288 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB6, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AB7, first strand: chain 'B' and resid 810 through 813 removed outlier: 3.667A pdb=" N GLU B 812 " --> pdb=" O ALA B 803 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA B 887 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP B 867 " --> pdb=" O ALA B 887 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1066 through 1068 removed outlier: 3.593A pdb=" N LYS B1074 " --> pdb=" O ALA B1082 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1066 through 1068 removed outlier: 3.682A pdb=" N GLU B1148 " --> pdb=" O ILE B1083 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B1085 " --> pdb=" O ILE B1146 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1929 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3878 1.34 - 1.45: 2307 1.45 - 1.57: 7534 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 13887 Sorted by residual: bond pdb=" CAO O6E A1201 " pdb=" CBO O6E A1201 " ideal model delta sigma weight residual 1.397 1.528 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" CAO O6E B1201 " pdb=" CBO O6E B1201 " ideal model delta sigma weight residual 1.397 1.517 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.530 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" CAV O6E B1201 " pdb=" NAE O6E B1201 " ideal model delta sigma weight residual 1.374 1.456 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" CAY O6E A1201 " pdb=" NAN O6E A1201 " ideal model delta sigma weight residual 1.346 1.423 -0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 13882 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 17791 2.04 - 4.08: 817 4.08 - 6.12: 119 6.12 - 8.16: 29 8.16 - 10.20: 14 Bond angle restraints: 18770 Sorted by residual: angle pdb=" C CYS A 842 " pdb=" N MET A 843 " pdb=" CA MET A 843 " ideal model delta sigma weight residual 121.56 127.70 -6.14 1.56e+00 4.11e-01 1.55e+01 angle pdb=" N MET A 843 " pdb=" CA MET A 843 " pdb=" C MET A 843 " ideal model delta sigma weight residual 110.42 115.85 -5.43 1.46e+00 4.69e-01 1.38e+01 angle pdb=" C ASP B 281 " pdb=" N GLU B 282 " pdb=" CA GLU B 282 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N GLY B 846 " pdb=" CA GLY B 846 " pdb=" C GLY B 846 " ideal model delta sigma weight residual 115.22 119.80 -4.58 1.27e+00 6.20e-01 1.30e+01 angle pdb=" C SER B1107 " pdb=" N SER B1108 " pdb=" CA SER B1108 " ideal model delta sigma weight residual 124.82 131.20 -6.38 1.78e+00 3.16e-01 1.28e+01 ... (remaining 18765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7477 17.98 - 35.95: 772 35.95 - 53.93: 163 53.93 - 71.91: 28 71.91 - 89.89: 16 Dihedral angle restraints: 8456 sinusoidal: 3478 harmonic: 4978 Sorted by residual: dihedral pdb=" CA GLU A1031 " pdb=" C GLU A1031 " pdb=" N ILE A1032 " pdb=" CA ILE A1032 " ideal model delta harmonic sigma weight residual 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA SER A1034 " pdb=" C SER A1034 " pdb=" N ILE A1035 " pdb=" CA ILE A1035 " ideal model delta harmonic sigma weight residual -180.00 -156.69 -23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA MET A1128 " pdb=" C MET A1128 " pdb=" N ASN A1129 " pdb=" CA ASN A1129 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 8453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1670 0.066 - 0.133: 365 0.133 - 0.199: 45 0.199 - 0.265: 18 0.265 - 0.331: 3 Chirality restraints: 2101 Sorted by residual: chirality pdb=" CG LEU B 187 " pdb=" CB LEU B 187 " pdb=" CD1 LEU B 187 " pdb=" CD2 LEU B 187 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA PHE B 838 " pdb=" N PHE B 838 " pdb=" C PHE B 838 " pdb=" CB PHE B 838 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LEU A1116 " pdb=" N LEU A1116 " pdb=" C LEU A1116 " pdb=" CB LEU A1116 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2098 not shown) Planarity restraints: 2413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " 0.207 2.00e-02 2.50e+03 2.11e-01 1.11e+03 pdb=" CAP O6E A1201 " -0.323 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " -0.018 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " -0.186 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " -0.053 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " 0.049 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.475 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " -0.020 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " -0.169 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " -0.198 2.00e-02 2.50e+03 1.98e-01 9.82e+02 pdb=" CAP O6E B1201 " 0.300 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " 0.010 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " 0.178 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " 0.045 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " -0.048 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " -0.446 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " 0.022 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " 0.164 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAQ O6E A1201 " -0.067 2.00e-02 2.50e+03 6.56e-02 5.39e+01 pdb=" CAY O6E A1201 " 0.070 2.00e-02 2.50e+03 pdb=" CBJ O6E A1201 " 0.072 2.00e-02 2.50e+03 pdb=" CBN O6E A1201 " -0.083 2.00e-02 2.50e+03 pdb=" NBP O6E A1201 " 0.009 2.00e-02 2.50e+03 ... (remaining 2410 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4167 2.84 - 3.35: 12408 3.35 - 3.87: 23087 3.87 - 4.38: 26427 4.38 - 4.90: 45454 Nonbonded interactions: 111543 Sorted by model distance: nonbonded pdb=" O THR B 168 " pdb=" OG SER B 172 " model vdw 2.321 3.040 nonbonded pdb=" O SER B 393 " pdb=" OG SER B 393 " model vdw 2.326 3.040 nonbonded pdb=" O VAL B 264 " pdb=" OG1 THR B 268 " model vdw 2.327 3.040 nonbonded pdb=" O ASN B 378 " pdb=" ND2 ASN B 430 " model vdw 2.328 3.120 nonbonded pdb=" O ILE A 470 " pdb=" NE1 TRP A 552 " model vdw 2.347 3.120 ... (remaining 111538 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 102 through 220 or resid 227 through 620 or resid 778 thro \ ugh 1201)) selection = (chain 'B' and (resid 102 through 378 or resid 393 through 986 or resid 993 thro \ ugh 1201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.020 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.006 0.131 13889 Z= 0.313 Angle : 1.006 10.201 18770 Z= 0.553 Chirality : 0.058 0.331 2101 Planarity : 0.010 0.211 2413 Dihedral : 15.417 89.886 5230 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.88 % Allowed : 11.61 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.18), residues: 1701 helix: -1.21 (0.18), residues: 670 sheet: -1.56 (0.27), residues: 344 loop : -2.08 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 554 TYR 0.039 0.003 TYR A 487 PHE 0.041 0.003 PHE B1080 TRP 0.037 0.002 TRP A 563 HIS 0.012 0.002 HIS B1106 Details of bonding type rmsd covalent geometry : bond 0.00625 (13887) covalent geometry : angle 1.00635 (18770) hydrogen bonds : bond 0.17812 ( 667) hydrogen bonds : angle 8.14890 ( 1929) Misc. bond : bond 0.03107 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 301 time to evaluate : 0.517 Fit side-chains REVERT: A 979 ILE cc_start: 0.7161 (mt) cc_final: 0.6817 (mt) REVERT: B 336 GLN cc_start: 0.5618 (pt0) cc_final: 0.5228 (pm20) REVERT: B 431 MET cc_start: 0.7140 (mtp) cc_final: 0.6935 (mtt) REVERT: B 466 GLN cc_start: 0.5340 (tp40) cc_final: 0.5094 (tp40) REVERT: B 483 TYR cc_start: 0.5268 (t80) cc_final: 0.4865 (t80) REVERT: B 611 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.6116 (pt0) REVERT: B 817 MET cc_start: 0.7298 (mmm) cc_final: 0.7012 (mmm) REVERT: B 823 TRP cc_start: 0.7205 (m100) cc_final: 0.6847 (m100) REVERT: B 940 LYS cc_start: 0.7472 (mttp) cc_final: 0.7109 (tptm) REVERT: B 983 MET cc_start: 0.3602 (ptm) cc_final: 0.3398 (ptm) REVERT: B 1127 LEU cc_start: 0.7764 (tp) cc_final: 0.7295 (mt) outliers start: 13 outliers final: 4 residues processed: 311 average time/residue: 0.1342 time to fit residues: 59.4084 Evaluate side-chains 187 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 611 GLN Chi-restraints excluded: chain B residue 917 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS A 355 HIS A 404 HIS A 608 HIS A 882 GLN B 959 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132953 restraints weight = 18583.054| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.95 r_work: 0.3586 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13889 Z= 0.159 Angle : 0.675 9.675 18770 Z= 0.345 Chirality : 0.043 0.181 2101 Planarity : 0.005 0.069 2413 Dihedral : 6.910 89.838 1942 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.47 % Favored : 96.41 % Rotamer: Outliers : 2.30 % Allowed : 16.34 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.19), residues: 1701 helix: -0.33 (0.19), residues: 699 sheet: -1.48 (0.26), residues: 365 loop : -1.74 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 138 TYR 0.016 0.002 TYR A 487 PHE 0.018 0.002 PHE A 903 TRP 0.012 0.002 TRP A 813 HIS 0.005 0.001 HIS B1106 Details of bonding type rmsd covalent geometry : bond 0.00363 (13887) covalent geometry : angle 0.67515 (18770) hydrogen bonds : bond 0.04481 ( 667) hydrogen bonds : angle 6.15960 ( 1929) Misc. bond : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 998 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: A 1072 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5842 (pt) REVERT: A 1076 MET cc_start: 0.7839 (mtp) cc_final: 0.7408 (mtm) REVERT: A 1140 ARG cc_start: 0.6804 (mtt90) cc_final: 0.6053 (mtp180) REVERT: B 291 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8075 (pttp) REVERT: B 318 GLN cc_start: 0.7949 (mp10) cc_final: 0.7598 (mp10) REVERT: B 336 GLN cc_start: 0.6191 (pt0) cc_final: 0.5568 (pm20) REVERT: B 431 MET cc_start: 0.8359 (mtp) cc_final: 0.8154 (mtt) REVERT: B 579 MET cc_start: 0.7908 (mmt) cc_final: 0.7662 (mmt) REVERT: B 823 TRP cc_start: 0.7488 (m100) cc_final: 0.7186 (m100) REVERT: B 881 VAL cc_start: 0.7435 (OUTLIER) cc_final: 0.7211 (p) REVERT: B 896 LYS cc_start: 0.5708 (OUTLIER) cc_final: 0.5397 (ptpt) REVERT: B 940 LYS cc_start: 0.7563 (mttp) cc_final: 0.7054 (tptm) REVERT: B 1015 PHE cc_start: 0.7554 (t80) cc_final: 0.6772 (m-80) REVERT: B 1114 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7485 (tt0) outliers start: 34 outliers final: 17 residues processed: 220 average time/residue: 0.1225 time to fit residues: 39.5116 Evaluate side-chains 193 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 998 GLU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1099 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 63 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 40 optimal weight: 0.0270 chunk 119 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 chunk 137 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** B1023 GLN ** 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 = 0.4025 r_free = 0.4025 target = 0.160406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134194 restraints weight = 18647.871| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.96 r_work: 0.3603 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13889 Z= 0.126 Angle : 0.620 10.236 18770 Z= 0.310 Chirality : 0.042 0.155 2101 Planarity : 0.004 0.065 2413 Dihedral : 6.453 89.344 1937 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.11 % Allowed : 16.95 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.20), residues: 1701 helix: 0.18 (0.19), residues: 702 sheet: -1.42 (0.25), residues: 365 loop : -1.56 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 182 TYR 0.022 0.001 TYR B 487 PHE 0.017 0.002 PHE A 903 TRP 0.010 0.001 TRP B 813 HIS 0.008 0.001 HIS B1106 Details of bonding type rmsd covalent geometry : bond 0.00286 (13887) covalent geometry : angle 0.61989 (18770) hydrogen bonds : bond 0.03729 ( 667) hydrogen bonds : angle 5.74367 ( 1929) Misc. bond : bond 0.00071 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.507 Fit side-chains REVERT: A 416 TYR cc_start: 0.7814 (t80) cc_final: 0.7611 (t80) REVERT: A 965 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7649 (tt) REVERT: A 998 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: A 1014 MET cc_start: 0.7177 (tpp) cc_final: 0.6489 (ttt) REVERT: A 1072 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5623 (pt) REVERT: A 1076 MET cc_start: 0.7773 (mtp) cc_final: 0.7376 (mtm) REVERT: A 1140 ARG cc_start: 0.6706 (mtt90) cc_final: 0.6038 (mtm180) REVERT: B 216 LEU cc_start: 0.8766 (mp) cc_final: 0.8415 (mt) REVERT: B 291 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7980 (pttp) REVERT: B 336 GLN cc_start: 0.6260 (pt0) cc_final: 0.5614 (pm20) REVERT: B 579 MET cc_start: 0.7914 (mmt) cc_final: 0.7613 (mmt) REVERT: B 604 MET cc_start: 0.7694 (tpt) cc_final: 0.7260 (tpp) REVERT: B 823 TRP cc_start: 0.7451 (m100) cc_final: 0.7238 (m100) REVERT: B 881 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.7198 (p) REVERT: B 896 LYS cc_start: 0.5699 (OUTLIER) cc_final: 0.5436 (ptpt) REVERT: B 897 VAL cc_start: 0.7238 (OUTLIER) cc_final: 0.6970 (t) REVERT: B 1014 MET cc_start: 0.7601 (mmm) cc_final: 0.7399 (mmm) REVERT: B 1015 PHE cc_start: 0.7528 (t80) cc_final: 0.6786 (m-80) REVERT: B 1096 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7269 (mp) REVERT: B 1114 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7444 (tt0) REVERT: B 1127 LEU cc_start: 0.7963 (tp) cc_final: 0.7351 (mt) outliers start: 46 outliers final: 24 residues processed: 214 average time/residue: 0.1131 time to fit residues: 36.2106 Evaluate side-chains 202 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 998 GLU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 47 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 23 optimal weight: 0.0030 chunk 130 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 HIS B 556 HIS ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135162 restraints weight = 18775.024| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.82 r_work: 0.3608 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13889 Z= 0.130 Angle : 0.600 8.383 18770 Z= 0.300 Chirality : 0.041 0.176 2101 Planarity : 0.004 0.066 2413 Dihedral : 6.271 88.883 1936 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.04 % Allowed : 18.03 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.20), residues: 1701 helix: 0.48 (0.20), residues: 700 sheet: -1.23 (0.26), residues: 362 loop : -1.47 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 182 TYR 0.023 0.001 TYR B 487 PHE 0.019 0.002 PHE B 948 TRP 0.013 0.001 TRP B 813 HIS 0.009 0.001 HIS B1106 Details of bonding type rmsd covalent geometry : bond 0.00298 (13887) covalent geometry : angle 0.60023 (18770) hydrogen bonds : bond 0.03507 ( 667) hydrogen bonds : angle 5.48798 ( 1929) Misc. bond : bond 0.00061 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.560 Fit side-chains REVERT: A 262 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: A 486 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7362 (tptt) REVERT: A 854 MET cc_start: 0.8475 (mtm) cc_final: 0.8166 (mtp) REVERT: A 965 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7594 (tt) REVERT: A 998 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: A 1002 LEU cc_start: 0.8796 (tt) cc_final: 0.8516 (tt) REVERT: A 1014 MET cc_start: 0.7175 (tpp) cc_final: 0.6530 (ttt) REVERT: A 1072 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5555 (pt) REVERT: A 1076 MET cc_start: 0.7926 (mtp) cc_final: 0.7500 (mtm) REVERT: A 1140 ARG cc_start: 0.6696 (mtt90) cc_final: 0.6057 (mtp180) REVERT: B 120 MET cc_start: 0.8417 (tmm) cc_final: 0.8193 (ttt) REVERT: B 216 LEU cc_start: 0.8707 (mp) cc_final: 0.8358 (mt) REVERT: B 291 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7991 (pttp) REVERT: B 336 GLN cc_start: 0.6256 (pt0) cc_final: 0.5777 (pm20) REVERT: B 579 MET cc_start: 0.7825 (mmt) cc_final: 0.7509 (mmt) REVERT: B 604 MET cc_start: 0.7716 (tpt) cc_final: 0.7470 (tpp) REVERT: B 823 TRP cc_start: 0.7537 (m100) cc_final: 0.7309 (m100) REVERT: B 881 VAL cc_start: 0.7622 (OUTLIER) cc_final: 0.7414 (p) REVERT: B 896 LYS cc_start: 0.5658 (OUTLIER) cc_final: 0.5407 (ptpt) REVERT: B 897 VAL cc_start: 0.7295 (OUTLIER) cc_final: 0.6999 (t) REVERT: B 940 LYS cc_start: 0.7729 (mttp) cc_final: 0.6824 (tptm) REVERT: B 1015 PHE cc_start: 0.7539 (t80) cc_final: 0.6828 (m-80) outliers start: 45 outliers final: 22 residues processed: 211 average time/residue: 0.1178 time to fit residues: 36.9282 Evaluate side-chains 193 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 998 GLU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1085 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 72 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 67 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 882 GLN B 858 HIS B1023 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135213 restraints weight = 18760.134| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.84 r_work: 0.3612 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13889 Z= 0.128 Angle : 0.593 8.267 18770 Z= 0.295 Chirality : 0.041 0.159 2101 Planarity : 0.004 0.065 2413 Dihedral : 6.189 88.933 1936 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.17 % Allowed : 18.77 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1701 helix: 0.62 (0.20), residues: 700 sheet: -1.10 (0.26), residues: 362 loop : -1.39 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 182 TYR 0.024 0.001 TYR B 487 PHE 0.018 0.002 PHE B 948 TRP 0.017 0.001 TRP A1110 HIS 0.006 0.001 HIS B1106 Details of bonding type rmsd covalent geometry : bond 0.00295 (13887) covalent geometry : angle 0.59329 (18770) hydrogen bonds : bond 0.03391 ( 667) hydrogen bonds : angle 5.36639 ( 1929) Misc. bond : bond 0.00053 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7444 (tptt) REVERT: A 965 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7526 (tt) REVERT: A 998 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7139 (pm20) REVERT: A 1002 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8467 (tt) REVERT: A 1072 LEU cc_start: 0.5889 (OUTLIER) cc_final: 0.5615 (pt) REVERT: A 1076 MET cc_start: 0.7904 (mtp) cc_final: 0.7433 (mtm) REVERT: A 1140 ARG cc_start: 0.6665 (mtt90) cc_final: 0.6023 (mtp180) REVERT: B 120 MET cc_start: 0.8409 (tmm) cc_final: 0.8203 (ttt) REVERT: B 216 LEU cc_start: 0.8690 (mp) cc_final: 0.8392 (mt) REVERT: B 291 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7967 (pttp) REVERT: B 336 GLN cc_start: 0.6237 (pt0) cc_final: 0.5795 (pm20) REVERT: B 505 TRP cc_start: 0.8431 (t60) cc_final: 0.7991 (t60) REVERT: B 823 TRP cc_start: 0.7611 (m100) cc_final: 0.7388 (m100) REVERT: B 881 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7446 (p) REVERT: B 897 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.7052 (t) REVERT: B 940 LYS cc_start: 0.7619 (mttp) cc_final: 0.6767 (tptm) REVERT: B 983 MET cc_start: 0.2630 (ptm) cc_final: 0.2404 (ptp) REVERT: B 1015 PHE cc_start: 0.7441 (t80) cc_final: 0.6836 (m-80) REVERT: B 1063 GLU cc_start: 0.6844 (mp0) cc_final: 0.6442 (mp0) outliers start: 47 outliers final: 28 residues processed: 204 average time/residue: 0.1181 time to fit residues: 35.6443 Evaluate side-chains 197 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 998 GLU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1127 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 86 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 140 optimal weight: 0.0040 chunk 38 optimal weight: 3.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 882 GLN ** B1023 GLN ** 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 = 0.4038 r_free = 0.4038 target = 0.161752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137024 restraints weight = 18623.899| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.84 r_work: 0.3625 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13889 Z= 0.113 Angle : 0.574 8.356 18770 Z= 0.286 Chirality : 0.041 0.162 2101 Planarity : 0.004 0.064 2413 Dihedral : 6.074 87.707 1936 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.38 % Allowed : 18.97 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1701 helix: 0.77 (0.20), residues: 700 sheet: -0.98 (0.27), residues: 360 loop : -1.31 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 182 TYR 0.024 0.001 TYR B 487 PHE 0.021 0.001 PHE B 948 TRP 0.019 0.001 TRP A1110 HIS 0.006 0.001 HIS B1106 Details of bonding type rmsd covalent geometry : bond 0.00257 (13887) covalent geometry : angle 0.57438 (18770) hydrogen bonds : bond 0.03235 ( 667) hydrogen bonds : angle 5.22567 ( 1929) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7421 (tptt) REVERT: A 532 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8123 (mp) REVERT: A 854 MET cc_start: 0.8498 (mtm) cc_final: 0.8223 (mtp) REVERT: A 965 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7468 (tt) REVERT: A 1002 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8379 (tt) REVERT: A 1061 SER cc_start: 0.7898 (p) cc_final: 0.7543 (t) REVERT: A 1072 LEU cc_start: 0.5738 (OUTLIER) cc_final: 0.5485 (pt) REVERT: A 1076 MET cc_start: 0.7860 (mtp) cc_final: 0.7424 (mtm) REVERT: A 1140 ARG cc_start: 0.6754 (mtt90) cc_final: 0.6072 (mtp180) REVERT: B 291 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7897 (pttp) REVERT: B 336 GLN cc_start: 0.6320 (pt0) cc_final: 0.5799 (pm20) REVERT: B 823 TRP cc_start: 0.7602 (m100) cc_final: 0.7384 (m100) REVERT: B 881 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7392 (p) REVERT: B 896 LYS cc_start: 0.5682 (OUTLIER) cc_final: 0.5048 (mmtm) REVERT: B 897 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.7046 (t) REVERT: B 940 LYS cc_start: 0.7591 (mttp) cc_final: 0.6721 (tptm) REVERT: B 983 MET cc_start: 0.2677 (ptm) cc_final: 0.2454 (ptp) REVERT: B 1015 PHE cc_start: 0.7345 (t80) cc_final: 0.6790 (m-80) REVERT: B 1063 GLU cc_start: 0.6818 (mp0) cc_final: 0.6375 (mp0) outliers start: 50 outliers final: 30 residues processed: 208 average time/residue: 0.1155 time to fit residues: 35.9207 Evaluate side-chains 201 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1107 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 166 optimal weight: 0.1980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1023 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.161910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136665 restraints weight = 18584.980| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.83 r_work: 0.3621 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13889 Z= 0.116 Angle : 0.575 8.357 18770 Z= 0.286 Chirality : 0.041 0.157 2101 Planarity : 0.004 0.064 2413 Dihedral : 6.052 87.941 1936 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.58 % Allowed : 19.24 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1701 helix: 0.85 (0.20), residues: 694 sheet: -0.87 (0.27), residues: 360 loop : -1.26 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 182 TYR 0.021 0.001 TYR B 487 PHE 0.024 0.001 PHE B 948 TRP 0.023 0.001 TRP A1110 HIS 0.005 0.001 HIS B1106 Details of bonding type rmsd covalent geometry : bond 0.00266 (13887) covalent geometry : angle 0.57464 (18770) hydrogen bonds : bond 0.03194 ( 667) hydrogen bonds : angle 5.17406 ( 1929) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7329 (ptmm) REVERT: A 486 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7454 (tptt) REVERT: A 532 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8149 (mp) REVERT: A 798 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7572 (pt) REVERT: A 854 MET cc_start: 0.8481 (mtm) cc_final: 0.8163 (mtp) REVERT: A 1002 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8420 (tt) REVERT: A 1014 MET cc_start: 0.7042 (tpp) cc_final: 0.6503 (ttt) REVERT: A 1061 SER cc_start: 0.7818 (p) cc_final: 0.7396 (t) REVERT: A 1072 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5552 (pt) REVERT: A 1076 MET cc_start: 0.7800 (mtp) cc_final: 0.7385 (mtm) REVERT: A 1140 ARG cc_start: 0.6701 (mtt90) cc_final: 0.6136 (mtp180) REVERT: B 216 LEU cc_start: 0.8613 (mp) cc_final: 0.8341 (mt) REVERT: B 291 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7905 (pttp) REVERT: B 336 GLN cc_start: 0.6429 (pt0) cc_final: 0.5929 (pm20) REVERT: B 505 TRP cc_start: 0.8382 (t60) cc_final: 0.7964 (t60) REVERT: B 823 TRP cc_start: 0.7582 (m100) cc_final: 0.7365 (m100) REVERT: B 881 VAL cc_start: 0.7610 (OUTLIER) cc_final: 0.7404 (p) REVERT: B 896 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.4995 (mmtm) REVERT: B 897 VAL cc_start: 0.7390 (OUTLIER) cc_final: 0.7043 (t) REVERT: B 940 LYS cc_start: 0.7574 (mttp) cc_final: 0.6755 (tptm) REVERT: B 1015 PHE cc_start: 0.7289 (t80) cc_final: 0.6809 (m-80) REVERT: B 1063 GLU cc_start: 0.6923 (mp0) cc_final: 0.6469 (mp0) outliers start: 53 outliers final: 29 residues processed: 202 average time/residue: 0.1148 time to fit residues: 34.6081 Evaluate side-chains 196 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1127 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 110 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 169 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN B 109 GLN B1023 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.160423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135326 restraints weight = 18470.003| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.87 r_work: 0.3601 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13889 Z= 0.135 Angle : 0.598 9.286 18770 Z= 0.296 Chirality : 0.042 0.156 2101 Planarity : 0.004 0.064 2413 Dihedral : 6.124 89.739 1936 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.38 % Allowed : 19.58 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1701 helix: 0.83 (0.20), residues: 694 sheet: -0.83 (0.27), residues: 363 loop : -1.21 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 182 TYR 0.028 0.001 TYR B 487 PHE 0.023 0.001 PHE B 948 TRP 0.016 0.001 TRP A1110 HIS 0.004 0.001 HIS B1106 Details of bonding type rmsd covalent geometry : bond 0.00318 (13887) covalent geometry : angle 0.59812 (18770) hydrogen bonds : bond 0.03293 ( 667) hydrogen bonds : angle 5.21686 ( 1929) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7308 (ptmm) REVERT: A 486 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7574 (tptt) REVERT: A 532 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8132 (mp) REVERT: A 798 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7524 (pt) REVERT: A 898 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6368 (mt) REVERT: A 1002 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8410 (tt) REVERT: A 1014 MET cc_start: 0.7142 (tpp) cc_final: 0.6673 (ttt) REVERT: A 1061 SER cc_start: 0.7658 (p) cc_final: 0.7249 (t) REVERT: A 1072 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5688 (pt) REVERT: A 1076 MET cc_start: 0.7882 (mtp) cc_final: 0.7447 (mtm) REVERT: A 1140 ARG cc_start: 0.6653 (mtt90) cc_final: 0.6109 (mtp180) REVERT: B 291 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7969 (pttp) REVERT: B 336 GLN cc_start: 0.6555 (pt0) cc_final: 0.5999 (pm20) REVERT: B 881 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7523 (p) REVERT: B 896 LYS cc_start: 0.5647 (OUTLIER) cc_final: 0.5168 (mmtm) REVERT: B 897 VAL cc_start: 0.7457 (OUTLIER) cc_final: 0.7083 (t) REVERT: B 940 LYS cc_start: 0.7616 (mttp) cc_final: 0.6839 (tptm) REVERT: B 1015 PHE cc_start: 0.7178 (t80) cc_final: 0.6720 (m-80) REVERT: B 1063 GLU cc_start: 0.6936 (mp0) cc_final: 0.6467 (mp0) outliers start: 50 outliers final: 32 residues processed: 206 average time/residue: 0.1223 time to fit residues: 37.2001 Evaluate side-chains 201 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1107 SER Chi-restraints excluded: chain B residue 1127 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 0.0270 chunk 116 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN A1133 GLN B 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135724 restraints weight = 18542.059| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.95 r_work: 0.3610 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13889 Z= 0.123 Angle : 0.585 10.525 18770 Z= 0.289 Chirality : 0.041 0.199 2101 Planarity : 0.004 0.064 2413 Dihedral : 6.059 89.362 1936 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.11 % Allowed : 20.12 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1701 helix: 0.94 (0.20), residues: 689 sheet: -0.81 (0.27), residues: 363 loop : -1.11 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 182 TYR 0.025 0.001 TYR B 487 PHE 0.021 0.001 PHE B 948 TRP 0.014 0.001 TRP A1110 HIS 0.004 0.001 HIS B1106 Details of bonding type rmsd covalent geometry : bond 0.00286 (13887) covalent geometry : angle 0.58516 (18770) hydrogen bonds : bond 0.03213 ( 667) hydrogen bonds : angle 5.17699 ( 1929) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7306 (ptmm) REVERT: A 486 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7570 (tptt) REVERT: A 532 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8119 (mp) REVERT: A 798 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7532 (pt) REVERT: A 898 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.6318 (mt) REVERT: A 1002 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8385 (tt) REVERT: A 1014 MET cc_start: 0.6879 (tpp) cc_final: 0.6476 (ttt) REVERT: A 1061 SER cc_start: 0.7615 (p) cc_final: 0.7265 (t) REVERT: A 1072 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5711 (pt) REVERT: A 1076 MET cc_start: 0.7870 (mtp) cc_final: 0.7462 (mtm) REVERT: A 1127 LEU cc_start: 0.7567 (mt) cc_final: 0.7314 (mt) REVERT: A 1140 ARG cc_start: 0.6751 (mtt90) cc_final: 0.6122 (mtp180) REVERT: B 291 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7869 (pttp) REVERT: B 336 GLN cc_start: 0.6564 (pt0) cc_final: 0.6004 (pm20) REVERT: B 539 MET cc_start: 0.8343 (ttt) cc_final: 0.7730 (ttt) REVERT: B 881 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7495 (p) REVERT: B 896 LYS cc_start: 0.5691 (OUTLIER) cc_final: 0.5288 (mmtm) REVERT: B 897 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7110 (t) REVERT: B 940 LYS cc_start: 0.7658 (mttp) cc_final: 0.6986 (tptm) REVERT: B 1015 PHE cc_start: 0.7174 (t80) cc_final: 0.6750 (m-80) REVERT: B 1063 GLU cc_start: 0.6995 (mp0) cc_final: 0.6512 (mp0) outliers start: 46 outliers final: 33 residues processed: 204 average time/residue: 0.1227 time to fit residues: 36.8203 Evaluate side-chains 200 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1133 GLN Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1107 SER Chi-restraints excluded: chain B residue 1127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 139 optimal weight: 0.0770 chunk 161 optimal weight: 0.9980 chunk 113 optimal weight: 0.0020 overall best weight: 0.5546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN A1133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136821 restraints weight = 18647.983| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.84 r_work: 0.3618 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13889 Z= 0.119 Angle : 0.584 10.961 18770 Z= 0.288 Chirality : 0.041 0.156 2101 Planarity : 0.004 0.065 2413 Dihedral : 6.038 89.630 1936 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.77 % Allowed : 20.66 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.21), residues: 1701 helix: 0.94 (0.20), residues: 695 sheet: -0.83 (0.27), residues: 361 loop : -1.12 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 182 TYR 0.025 0.001 TYR B 487 PHE 0.022 0.001 PHE B 948 TRP 0.025 0.001 TRP B 505 HIS 0.003 0.001 HIS B1106 Details of bonding type rmsd covalent geometry : bond 0.00274 (13887) covalent geometry : angle 0.58428 (18770) hydrogen bonds : bond 0.03177 ( 667) hydrogen bonds : angle 5.15391 ( 1929) Misc. bond : bond 0.00035 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7312 (ptmm) REVERT: A 486 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7566 (tptt) REVERT: A 532 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 798 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7540 (pt) REVERT: A 898 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6357 (mt) REVERT: A 1002 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8402 (tt) REVERT: A 1014 MET cc_start: 0.6890 (tpp) cc_final: 0.6462 (ttt) REVERT: A 1061 SER cc_start: 0.7593 (p) cc_final: 0.7249 (t) REVERT: A 1072 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5696 (pt) REVERT: A 1076 MET cc_start: 0.7865 (mtp) cc_final: 0.7457 (mtm) REVERT: A 1127 LEU cc_start: 0.7552 (mt) cc_final: 0.7304 (mt) REVERT: A 1140 ARG cc_start: 0.6746 (mtt90) cc_final: 0.6120 (mtp180) REVERT: B 291 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7845 (pttp) REVERT: B 336 GLN cc_start: 0.6636 (pt0) cc_final: 0.5949 (pm20) REVERT: B 539 MET cc_start: 0.8340 (ttt) cc_final: 0.7728 (ttt) REVERT: B 881 VAL cc_start: 0.7687 (OUTLIER) cc_final: 0.7469 (p) REVERT: B 896 LYS cc_start: 0.5672 (OUTLIER) cc_final: 0.5280 (mmtm) REVERT: B 897 VAL cc_start: 0.7439 (OUTLIER) cc_final: 0.7080 (t) REVERT: B 940 LYS cc_start: 0.7680 (mttp) cc_final: 0.6954 (tptm) REVERT: B 1015 PHE cc_start: 0.7144 (t80) cc_final: 0.6701 (m-80) REVERT: B 1063 GLU cc_start: 0.6993 (mp0) cc_final: 0.6548 (mp0) outliers start: 41 outliers final: 31 residues processed: 198 average time/residue: 0.1268 time to fit residues: 37.1033 Evaluate side-chains 203 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1133 GLN Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 72 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 33 optimal weight: 0.0570 chunk 136 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 86 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN A1133 GLN B 466 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.162459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137630 restraints weight = 18610.607| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.83 r_work: 0.3622 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13889 Z= 0.114 Angle : 0.586 11.198 18770 Z= 0.290 Chirality : 0.041 0.211 2101 Planarity : 0.004 0.065 2413 Dihedral : 6.001 89.501 1936 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.97 % Allowed : 20.39 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1701 helix: 1.00 (0.20), residues: 695 sheet: -0.79 (0.27), residues: 360 loop : -1.11 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 182 TYR 0.024 0.001 TYR B 487 PHE 0.022 0.001 PHE B 948 TRP 0.026 0.002 TRP A1110 HIS 0.003 0.001 HIS B1106 Details of bonding type rmsd covalent geometry : bond 0.00262 (13887) covalent geometry : angle 0.58564 (18770) hydrogen bonds : bond 0.03115 ( 667) hydrogen bonds : angle 5.11364 ( 1929) Misc. bond : bond 0.00031 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3630.05 seconds wall clock time: 62 minutes 48.89 seconds (3768.89 seconds total)