Starting phenix.real_space_refine on Fri May 23 12:35:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8soa_40651/05_2025/8soa_40651_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8soa_40651/05_2025/8soa_40651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8soa_40651/05_2025/8soa_40651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8soa_40651/05_2025/8soa_40651.map" model { file = "/net/cci-nas-00/data/ceres_data/8soa_40651/05_2025/8soa_40651_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8soa_40651/05_2025/8soa_40651_trim.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 61 5.16 5 C 7684 2.51 5 N 2045 2.21 5 O 2180 1.98 5 H 12066 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24039 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 16081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 16081 Classifications: {'peptide': 984} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 940} Chain breaks: 8 Chain: "B" Number of atoms: 7927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7927 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 472} Chain breaks: 8 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.35, per 1000 atoms: 0.47 Number of scatterers: 24039 At special positions: 0 Unit cell: (103.68, 101.52, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 61 16.00 P 3 15.00 O 2180 8.00 N 2045 7.00 C 7684 6.00 H 12066 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.43 Conformation dependent library (CDL) restraints added in 1.9 seconds 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2834 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 12 sheets defined 49.1% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.936A pdb=" N TYR A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 118 Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.767A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 180 through 189 removed outlier: 3.699A pdb=" N ARG A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.785A pdb=" N LYS A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.848A pdb=" N GLN A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.889A pdb=" N GLU A 317 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.564A pdb=" N LEU A 502 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 503 " --> pdb=" O ASP A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 503' Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 568 through 578 Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 588 through 593 Processing helix chain 'A' and resid 600 through 613 removed outlier: 4.368A pdb=" N LYS A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 630 Processing helix chain 'A' and resid 638 through 649 removed outlier: 3.673A pdb=" N ALA A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 removed outlier: 3.785A pdb=" N HIS A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 659 " --> pdb=" O ASP A 655 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLN A 662 " --> pdb=" O HIS A 658 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.576A pdb=" N GLY A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 701 " --> pdb=" O TRP A 697 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 725 removed outlier: 4.174A pdb=" N GLY A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 752 removed outlier: 3.531A pdb=" N GLN A 735 " --> pdb=" O ASP A 731 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 845 through 858 removed outlier: 3.845A pdb=" N ARG A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 892 Processing helix chain 'A' and resid 905 through 915 removed outlier: 3.646A pdb=" N HIS A 909 " --> pdb=" O GLU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 942 removed outlier: 3.543A pdb=" N ARG A 927 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 934 " --> pdb=" O TYR A 930 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 940 " --> pdb=" O CYS A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 988 through 994 removed outlier: 3.731A pdb=" N LEU A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.668A pdb=" N LYS A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A1022 " --> pdb=" O LEU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1038 Processing helix chain 'A' and resid 1049 through 1054 Processing helix chain 'A' and resid 1060 through 1066 Processing helix chain 'A' and resid 1066 through 1079 Processing helix chain 'A' and resid 1081 through 1092 Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 51 through 71 removed outlier: 4.196A pdb=" N PHE B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.624A pdb=" N LEU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 removed outlier: 3.759A pdb=" N ARG B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 188 through 206 removed outlier: 3.739A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 220 removed outlier: 3.835A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 removed outlier: 3.733A pdb=" N GLY B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.661A pdb=" N GLN B 302 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 543 removed outlier: 4.051A pdb=" N LYS B 528 " --> pdb=" O ARG B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 605 through 613 Processing helix chain 'B' and resid 613 through 620 Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 696 through 702 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 61 removed outlier: 4.328A pdb=" N GLY A 133 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 137 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N GLN A 134 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLN A 101 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 235 removed outlier: 4.054A pdb=" N ILE A 303 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 272 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.391A pdb=" N VAL A 352 " --> pdb=" O ALA A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 419 removed outlier: 6.527A pdb=" N ARG A 366 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL A 412 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS A 364 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 414 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG A 362 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE A 416 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS A 360 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER A 517 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE A 368 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER A 515 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 395 removed outlier: 5.299A pdb=" N VAL A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A 389 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS A 395 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 395 removed outlier: 5.299A pdb=" N VAL A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A 389 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS A 395 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 462 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N CYS A 435 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 460 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 783 through 785 removed outlier: 6.143A pdb=" N LEU A 791 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS A 816 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU A 796 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLU A 814 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AA9, first strand: chain 'B' and resid 288 through 289 removed outlier: 8.863A pdb=" N TYR B 289 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR B 162 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 161 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.733A pdb=" N ILE B 869 " --> pdb=" O VAL B 667 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 683 through 688 removed outlier: 3.911A pdb=" N LYS B 732 " --> pdb=" O ARG B 740 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 795 through 799 removed outlier: 3.591A pdb=" N SER B 795 " --> pdb=" O LEU B 774 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 695 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA B 813 " --> pdb=" O GLY B 695 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1659 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: 9.27 Time building geometry restraints manager: 7.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12030 1.03 - 1.23: 41 1.23 - 1.42: 5037 1.42 - 1.62: 7105 1.62 - 1.81: 86 Bond restraints: 24299 Sorted by residual: bond pdb=" N THR B 7 " pdb=" CA THR B 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N LEU A 37 " pdb=" CA LEU A 37 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N THR B 7 " pdb=" H THR B 7 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" N LEU A 37 " pdb=" H LEU A 37 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" CB PRO B 868 " pdb=" CG PRO B 868 " ideal model delta sigma weight residual 1.492 1.550 -0.058 5.00e-02 4.00e+02 1.35e+00 ... (remaining 24294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 43524 1.84 - 3.68: 424 3.68 - 5.51: 43 5.51 - 7.35: 7 7.35 - 9.19: 2 Bond angle restraints: 44000 Sorted by residual: angle pdb=" N VAL B 529 " pdb=" CA VAL B 529 " pdb=" C VAL B 529 " ideal model delta sigma weight residual 110.30 103.59 6.71 9.70e-01 1.06e+00 4.78e+01 angle pdb=" N ILE A 891 " pdb=" CA ILE A 891 " pdb=" C ILE A 891 " ideal model delta sigma weight residual 112.98 107.83 5.15 1.25e+00 6.40e-01 1.70e+01 angle pdb=" CA VAL A 983 " pdb=" C VAL A 983 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 116.57 119.40 -2.83 9.80e-01 1.04e+00 8.35e+00 angle pdb=" N ARG B 538 " pdb=" CA ARG B 538 " pdb=" C ARG B 538 " ideal model delta sigma weight residual 112.89 109.50 3.39 1.24e+00 6.50e-01 7.47e+00 angle pdb=" N VAL B 517 " pdb=" CA VAL B 517 " pdb=" C VAL B 517 " ideal model delta sigma weight residual 108.36 104.48 3.88 1.43e+00 4.89e-01 7.37e+00 ... (remaining 43995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 10646 17.58 - 35.15: 489 35.15 - 52.73: 184 52.73 - 70.30: 63 70.30 - 87.88: 7 Dihedral angle restraints: 11389 sinusoidal: 6239 harmonic: 5150 Sorted by residual: dihedral pdb=" CD ARG A 700 " pdb=" NE ARG A 700 " pdb=" CZ ARG A 700 " pdb=" NH1 ARG A 700 " ideal model delta sinusoidal sigma weight residual 0.00 43.40 -43.40 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CA VAL B 519 " pdb=" C VAL B 519 " pdb=" N PHE B 520 " pdb=" CA PHE B 520 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA VAL A1057 " pdb=" C VAL A1057 " pdb=" N GLY A1058 " pdb=" CA GLY A1058 " ideal model delta harmonic sigma weight residual -180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 11386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1649 0.060 - 0.120: 207 0.120 - 0.179: 31 0.179 - 0.239: 1 0.239 - 0.299: 2 Chirality restraints: 1890 Sorted by residual: chirality pdb=" C2' ATP A1201 " pdb=" C1' ATP A1201 " pdb=" C3' ATP A1201 " pdb=" O2' ATP A1201 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C3' ATP A1201 " pdb=" C2' ATP A1201 " pdb=" C4' ATP A1201 " pdb=" O3' ATP A1201 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C4' ATP A1201 " pdb=" C3' ATP A1201 " pdb=" C5' ATP A1201 " pdb=" O4' ATP A1201 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1887 not shown) Planarity restraints: 3481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 700 " -0.633 9.50e-02 1.11e+02 2.12e-01 5.59e+01 pdb=" NE ARG A 700 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A 700 " -0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 700 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 700 " 0.019 2.00e-02 2.50e+03 pdb="HH11 ARG A 700 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 700 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 700 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 700 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 155 " -0.021 2.00e-02 2.50e+03 2.53e-02 9.63e+00 pdb=" CG ASN A 155 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 155 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 155 " 0.040 2.00e-02 2.50e+03 pdb="HD21 ASN A 155 " -0.000 2.00e-02 2.50e+03 pdb="HD22 ASN A 155 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 151 " 0.021 2.00e-02 2.50e+03 2.50e-02 9.38e+00 pdb=" CD GLN A 151 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN A 151 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN A 151 " -0.040 2.00e-02 2.50e+03 pdb="HE21 GLN A 151 " -0.000 2.00e-02 2.50e+03 pdb="HE22 GLN A 151 " 0.038 2.00e-02 2.50e+03 ... (remaining 3478 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1103 2.18 - 2.79: 49239 2.79 - 3.39: 63501 3.39 - 4.00: 82374 4.00 - 4.60: 130744 Nonbonded interactions: 326961 Sorted by model distance: nonbonded pdb=" OD1 ASN A 66 " pdb=" H GLN A 69 " model vdw 1.576 2.450 nonbonded pdb="HH21 ARG A 178 " pdb=" O PRO A 324 " model vdw 1.605 2.450 nonbonded pdb=" OD2 ASP A 674 " pdb="HH21 ARG A 679 " model vdw 1.608 2.450 nonbonded pdb=" OD2 ASP B 245 " pdb=" H GLU B 248 " model vdw 1.608 2.450 nonbonded pdb=" OE1 GLU A 337 " pdb="HH21 ARG A 533 " model vdw 1.609 2.450 ... (remaining 326956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 50.770 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 0.004 0.058 12233 Z= 0.176 Angle : 0.634 9.190 16577 Z= 0.346 Chirality : 0.043 0.299 1890 Planarity : 0.007 0.271 2085 Dihedral : 13.198 87.876 4561 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.37 % Favored : 93.36 % Rotamer: Outliers : 4.83 % Allowed : 7.01 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1445 helix: -0.31 (0.21), residues: 646 sheet: -1.28 (0.33), residues: 237 loop : -0.97 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 812 HIS 0.007 0.001 HIS A 169 PHE 0.029 0.002 PHE A1009 TYR 0.025 0.002 TYR A 389 ARG 0.048 0.001 ARG A 700 Details of bonding type rmsd hydrogen bonds : bond 0.23821 ( 579) hydrogen bonds : angle 7.94672 ( 1659) covalent geometry : bond 0.00398 (12233) covalent geometry : angle 0.63378 (16577) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7785 (t80) REVERT: A 431 LEU cc_start: 0.8139 (mt) cc_final: 0.7682 (mt) REVERT: A 498 ASN cc_start: 0.7924 (t0) cc_final: 0.7682 (t0) REVERT: A 581 GLU cc_start: 0.6076 (tp30) cc_final: 0.5709 (mp0) REVERT: A 993 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6674 (m-80) REVERT: A 1055 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6927 (tt) REVERT: A 1062 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7834 (mm-30) REVERT: B 239 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9073 (tt) REVERT: B 516 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6691 (mtm180) REVERT: B 611 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.6022 (pmm) outliers start: 64 outliers final: 31 residues processed: 275 average time/residue: 0.6761 time to fit residues: 253.2139 Evaluate side-chains 161 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1089 HIS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 516 ARG Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 773 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.5980 chunk 111 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.0060 chunk 59 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 151 GLN A 391 GLN A 522 ASN A 959 ASN B 70 GLN B 156 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.142980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.105686 restraints weight = 58133.210| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.83 r_work: 0.3644 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12233 Z= 0.162 Angle : 0.610 5.626 16577 Z= 0.320 Chirality : 0.042 0.193 1890 Planarity : 0.005 0.040 2085 Dihedral : 8.789 78.779 1693 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.70 % Allowed : 10.94 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1445 helix: 0.16 (0.20), residues: 674 sheet: -1.22 (0.34), residues: 225 loop : -0.94 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1080 HIS 0.005 0.001 HIS A 199 PHE 0.018 0.002 PHE A 696 TYR 0.018 0.001 TYR A 935 ARG 0.006 0.001 ARG A1052 Details of bonding type rmsd hydrogen bonds : bond 0.06176 ( 579) hydrogen bonds : angle 5.55811 ( 1659) covalent geometry : bond 0.00361 (12233) covalent geometry : angle 0.60987 (16577) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TRP cc_start: 0.7648 (m-10) cc_final: 0.7245 (m-10) REVERT: A 248 PHE cc_start: 0.7764 (t80) cc_final: 0.7508 (t80) REVERT: A 249 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7960 (t80) REVERT: A 428 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 547 MET cc_start: 0.7185 (ptp) cc_final: 0.6846 (ptp) REVERT: A 581 GLU cc_start: 0.6024 (tp30) cc_final: 0.5577 (mp0) REVERT: A 851 MET cc_start: 0.7372 (mtp) cc_final: 0.7141 (mtp) REVERT: A 993 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: A 998 SER cc_start: 0.7737 (p) cc_final: 0.7465 (m) REVERT: A 1055 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7075 (tt) REVERT: A 1084 PHE cc_start: 0.8496 (t80) cc_final: 0.7879 (t80) REVERT: B 239 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9010 (tt) REVERT: B 730 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.6591 (p90) outliers start: 49 outliers final: 32 residues processed: 168 average time/residue: 0.6188 time to fit residues: 143.7909 Evaluate side-chains 145 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN A 769 GLN A 773 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.141936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.104394 restraints weight = 58230.138| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.85 r_work: 0.3628 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12233 Z= 0.179 Angle : 0.571 6.978 16577 Z= 0.299 Chirality : 0.042 0.187 1890 Planarity : 0.004 0.039 2085 Dihedral : 7.838 89.949 1664 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.39 % Allowed : 11.16 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1445 helix: 0.23 (0.20), residues: 681 sheet: -1.37 (0.33), residues: 234 loop : -0.95 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1080 HIS 0.012 0.001 HIS A1089 PHE 0.019 0.002 PHE A 696 TYR 0.021 0.002 TYR A 935 ARG 0.004 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.05415 ( 579) hydrogen bonds : angle 5.25488 ( 1659) covalent geometry : bond 0.00415 (12233) covalent geometry : angle 0.57052 (16577) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.8088 (t80) REVERT: A 428 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8139 (mp) REVERT: A 547 MET cc_start: 0.7079 (ptp) cc_final: 0.6767 (ptp) REVERT: A 581 GLU cc_start: 0.6022 (tp30) cc_final: 0.5563 (mp0) REVERT: A 903 LYS cc_start: 0.8491 (tptm) cc_final: 0.8044 (tptp) REVERT: A 993 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: A 998 SER cc_start: 0.7831 (p) cc_final: 0.7529 (m) REVERT: A 1033 MET cc_start: 0.7197 (mtt) cc_final: 0.6943 (mtp) REVERT: A 1055 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7043 (tt) REVERT: A 1084 PHE cc_start: 0.8605 (t80) cc_final: 0.8026 (t80) REVERT: B 239 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8953 (tt) REVERT: B 730 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6512 (p90) outliers start: 45 outliers final: 35 residues processed: 143 average time/residue: 0.5998 time to fit residues: 120.8288 Evaluate side-chains 145 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 773 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 76 optimal weight: 0.0770 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.143442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.108850 restraints weight = 58655.099| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.07 r_work: 0.3648 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12233 Z= 0.122 Angle : 0.509 5.591 16577 Z= 0.263 Chirality : 0.040 0.167 1890 Planarity : 0.004 0.044 2085 Dihedral : 7.353 75.532 1660 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.17 % Allowed : 11.16 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1445 helix: 0.62 (0.20), residues: 677 sheet: -1.24 (0.33), residues: 235 loop : -0.82 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1080 HIS 0.007 0.001 HIS A 693 PHE 0.014 0.001 PHE A 696 TYR 0.013 0.001 TYR A 935 ARG 0.006 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 579) hydrogen bonds : angle 4.85408 ( 1659) covalent geometry : bond 0.00275 (12233) covalent geometry : angle 0.50859 (16577) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.8095 (pt0) cc_final: 0.7839 (pt0) REVERT: A 249 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.8121 (t80) REVERT: A 428 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 547 MET cc_start: 0.7076 (ptp) cc_final: 0.6790 (ptp) REVERT: A 581 GLU cc_start: 0.6012 (tp30) cc_final: 0.5586 (mp0) REVERT: A 700 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7265 (mtt-85) REVERT: A 903 LYS cc_start: 0.8492 (tptm) cc_final: 0.8061 (tptp) REVERT: A 993 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.6889 (m-80) REVERT: A 998 SER cc_start: 0.7796 (p) cc_final: 0.7471 (m) REVERT: A 1055 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.6980 (tt) REVERT: B 239 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8902 (tt) REVERT: B 730 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6628 (p90) outliers start: 42 outliers final: 31 residues processed: 140 average time/residue: 0.5437 time to fit residues: 110.4169 Evaluate side-chains 139 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 773 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.142777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.104866 restraints weight = 58609.304| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.91 r_work: 0.3631 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12233 Z= 0.141 Angle : 0.513 6.141 16577 Z= 0.265 Chirality : 0.040 0.152 1890 Planarity : 0.004 0.048 2085 Dihedral : 7.066 65.257 1653 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.02 % Allowed : 11.92 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1445 helix: 0.67 (0.20), residues: 679 sheet: -1.23 (0.33), residues: 235 loop : -0.88 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1080 HIS 0.005 0.001 HIS A 693 PHE 0.017 0.001 PHE A 696 TYR 0.016 0.001 TYR A 935 ARG 0.006 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 579) hydrogen bonds : angle 4.75668 ( 1659) covalent geometry : bond 0.00327 (12233) covalent geometry : angle 0.51348 (16577) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8172 (t80) REVERT: A 428 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8156 (mp) REVERT: A 547 MET cc_start: 0.7095 (ptp) cc_final: 0.6824 (ptp) REVERT: A 581 GLU cc_start: 0.5940 (tp30) cc_final: 0.5504 (mp0) REVERT: A 903 LYS cc_start: 0.8501 (tptm) cc_final: 0.8078 (tptp) REVERT: A 993 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.6913 (m-80) REVERT: A 998 SER cc_start: 0.7852 (p) cc_final: 0.7514 (m) REVERT: A 1033 MET cc_start: 0.7249 (mtt) cc_final: 0.6982 (mtp) REVERT: A 1055 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6998 (tt) REVERT: B 239 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8886 (tt) REVERT: B 730 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6708 (p90) outliers start: 40 outliers final: 31 residues processed: 134 average time/residue: 0.5588 time to fit residues: 109.9520 Evaluate side-chains 137 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 773 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.143074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.108368 restraints weight = 58039.006| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.79 r_work: 0.3655 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12233 Z= 0.126 Angle : 0.495 5.825 16577 Z= 0.255 Chirality : 0.040 0.151 1890 Planarity : 0.004 0.053 2085 Dihedral : 6.895 59.633 1652 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.79 % Allowed : 11.99 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1445 helix: 0.82 (0.20), residues: 681 sheet: -1.25 (0.33), residues: 235 loop : -0.81 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1080 HIS 0.007 0.001 HIS A 693 PHE 0.015 0.001 PHE A 696 TYR 0.013 0.001 TYR A 935 ARG 0.008 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 579) hydrogen bonds : angle 4.60111 ( 1659) covalent geometry : bond 0.00292 (12233) covalent geometry : angle 0.49533 (16577) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.8169 (t80) REVERT: A 428 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8114 (mp) REVERT: A 547 MET cc_start: 0.7097 (ptp) cc_final: 0.6833 (ptp) REVERT: A 581 GLU cc_start: 0.6003 (tp30) cc_final: 0.5583 (mp0) REVERT: A 903 LYS cc_start: 0.8488 (tptm) cc_final: 0.8065 (tptp) REVERT: A 993 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: A 998 SER cc_start: 0.7856 (p) cc_final: 0.7508 (m) REVERT: A 1033 MET cc_start: 0.7255 (mtt) cc_final: 0.6980 (mtp) REVERT: A 1055 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6971 (tt) REVERT: B 239 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8844 (tt) REVERT: B 730 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6677 (p90) outliers start: 37 outliers final: 27 residues processed: 130 average time/residue: 0.5316 time to fit residues: 100.0941 Evaluate side-chains 133 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 809 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 145 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.140293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.103970 restraints weight = 59309.105| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 3.05 r_work: 0.3588 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12233 Z= 0.252 Angle : 0.585 7.894 16577 Z= 0.307 Chirality : 0.043 0.150 1890 Planarity : 0.005 0.052 2085 Dihedral : 7.071 59.275 1648 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.24 % Allowed : 11.92 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1445 helix: 0.44 (0.20), residues: 676 sheet: -1.27 (0.34), residues: 225 loop : -1.27 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 617 HIS 0.007 0.001 HIS A 199 PHE 0.024 0.002 PHE A 696 TYR 0.023 0.002 TYR A 935 ARG 0.008 0.001 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 579) hydrogen bonds : angle 4.94951 ( 1659) covalent geometry : bond 0.00590 (12233) covalent geometry : angle 0.58513 (16577) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8280 (t80) REVERT: A 428 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8180 (mp) REVERT: A 547 MET cc_start: 0.7163 (ptp) cc_final: 0.6890 (ptp) REVERT: A 581 GLU cc_start: 0.6045 (tp30) cc_final: 0.5571 (mp0) REVERT: A 993 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.6989 (m-80) REVERT: A 1033 MET cc_start: 0.7160 (mtt) cc_final: 0.6889 (mtp) REVERT: A 1036 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5574 (mmp) REVERT: A 1055 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7100 (tt) REVERT: B 64 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8440 (mm-40) REVERT: B 239 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8968 (tt) REVERT: B 730 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.6842 (p90) outliers start: 43 outliers final: 34 residues processed: 129 average time/residue: 0.5146 time to fit residues: 98.5230 Evaluate side-chains 133 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 809 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 122 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.142178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.104307 restraints weight = 58258.092| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.93 r_work: 0.3622 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12233 Z= 0.126 Angle : 0.506 6.330 16577 Z= 0.261 Chirality : 0.040 0.152 1890 Planarity : 0.004 0.060 2085 Dihedral : 6.898 58.589 1648 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.87 % Allowed : 12.75 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1445 helix: 0.73 (0.20), residues: 681 sheet: -1.34 (0.33), residues: 237 loop : -1.07 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1080 HIS 0.007 0.001 HIS A 693 PHE 0.016 0.001 PHE A 696 TYR 0.014 0.001 TYR A 935 ARG 0.009 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 579) hydrogen bonds : angle 4.60687 ( 1659) covalent geometry : bond 0.00292 (12233) covalent geometry : angle 0.50561 (16577) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8276 (t80) REVERT: A 428 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8150 (mp) REVERT: A 547 MET cc_start: 0.7101 (ptp) cc_final: 0.6828 (ptp) REVERT: A 581 GLU cc_start: 0.5944 (tp30) cc_final: 0.5500 (mp0) REVERT: A 717 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7001 (tp) REVERT: A 993 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: A 998 SER cc_start: 0.7958 (p) cc_final: 0.7611 (m) REVERT: A 1033 MET cc_start: 0.7134 (mtt) cc_final: 0.6840 (mtp) REVERT: A 1055 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7024 (tt) REVERT: B 64 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8411 (mm-40) REVERT: B 239 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8862 (tt) REVERT: B 730 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.6941 (p90) outliers start: 38 outliers final: 29 residues processed: 125 average time/residue: 0.5455 time to fit residues: 99.8896 Evaluate side-chains 131 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 809 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 110 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.143036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.105379 restraints weight = 58201.857| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.89 r_work: 0.3646 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12233 Z= 0.112 Angle : 0.483 5.570 16577 Z= 0.247 Chirality : 0.039 0.150 1890 Planarity : 0.004 0.068 2085 Dihedral : 6.708 57.885 1648 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.71 % Allowed : 12.97 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), residues: 1445 helix: 1.03 (0.20), residues: 679 sheet: -1.22 (0.33), residues: 237 loop : -0.89 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1080 HIS 0.008 0.001 HIS A 693 PHE 0.022 0.001 PHE B 550 TYR 0.012 0.001 TYR A 935 ARG 0.011 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 579) hydrogen bonds : angle 4.43859 ( 1659) covalent geometry : bond 0.00261 (12233) covalent geometry : angle 0.48260 (16577) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8124 (mp) REVERT: A 547 MET cc_start: 0.7179 (ptp) cc_final: 0.6903 (ptp) REVERT: A 581 GLU cc_start: 0.5960 (tp30) cc_final: 0.5540 (mp0) REVERT: A 993 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: A 998 SER cc_start: 0.7924 (p) cc_final: 0.7571 (m) REVERT: A 1055 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6994 (tt) REVERT: B 239 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8843 (tt) REVERT: B 730 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7030 (p90) outliers start: 36 outliers final: 29 residues processed: 128 average time/residue: 0.5442 time to fit residues: 103.6004 Evaluate side-chains 129 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 809 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 140 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 50 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.142928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.105088 restraints weight = 58520.603| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.94 r_work: 0.3635 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12233 Z= 0.115 Angle : 0.488 5.818 16577 Z= 0.249 Chirality : 0.039 0.149 1890 Planarity : 0.004 0.064 2085 Dihedral : 6.666 58.363 1648 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.64 % Allowed : 13.35 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.23), residues: 1445 helix: 1.09 (0.20), residues: 679 sheet: -1.22 (0.33), residues: 238 loop : -0.86 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1080 HIS 0.008 0.001 HIS A 693 PHE 0.015 0.001 PHE A 696 TYR 0.013 0.001 TYR A 935 ARG 0.010 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 579) hydrogen bonds : angle 4.41704 ( 1659) covalent geometry : bond 0.00268 (12233) covalent geometry : angle 0.48805 (16577) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8109 (mp) REVERT: A 547 MET cc_start: 0.7180 (ptp) cc_final: 0.6912 (ptp) REVERT: A 581 GLU cc_start: 0.5931 (tp30) cc_final: 0.5495 (mp0) REVERT: A 993 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: A 998 SER cc_start: 0.7944 (p) cc_final: 0.7587 (m) REVERT: A 1036 MET cc_start: 0.5783 (mtp) cc_final: 0.5274 (mmp) REVERT: A 1055 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7008 (tt) REVERT: B 239 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8881 (tt) REVERT: B 730 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7014 (p90) outliers start: 35 outliers final: 30 residues processed: 124 average time/residue: 0.5139 time to fit residues: 93.5311 Evaluate side-chains 131 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 809 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.0020 chunk 130 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.142988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.105119 restraints weight = 58366.993| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.95 r_work: 0.3637 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12233 Z= 0.113 Angle : 0.483 5.504 16577 Z= 0.246 Chirality : 0.039 0.149 1890 Planarity : 0.004 0.041 2085 Dihedral : 6.520 58.795 1646 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.56 % Allowed : 13.42 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.23), residues: 1445 helix: 1.16 (0.20), residues: 679 sheet: -1.18 (0.33), residues: 238 loop : -0.83 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1080 HIS 0.008 0.001 HIS A 693 PHE 0.015 0.001 PHE A 696 TYR 0.013 0.001 TYR A 935 ARG 0.005 0.000 ARG A 784 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 579) hydrogen bonds : angle 4.35948 ( 1659) covalent geometry : bond 0.00264 (12233) covalent geometry : angle 0.48276 (16577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13490.62 seconds wall clock time: 231 minutes 36.36 seconds (13896.36 seconds total)