Starting phenix.real_space_refine on Mon Aug 25 00:57:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8soa_40651/08_2025/8soa_40651_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8soa_40651/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8soa_40651/08_2025/8soa_40651_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8soa_40651/08_2025/8soa_40651_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8soa_40651/08_2025/8soa_40651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8soa_40651/08_2025/8soa_40651.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.28, per 1000 atoms: 0.14 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: 2.08 Conformation dependent library (CDL) restraints added in 562.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.63 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: 4.58 Time building geometry restraints manager: 2.88 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: 1.780 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: 0.110 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.730 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.048 0.001 ARG A 700 TYR 0.025 0.002 TYR A 389 PHE 0.029 0.002 PHE A1009 TRP 0.012 0.001 TRP A 812 HIS 0.007 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00398 (12233) covalent geometry : angle 0.63378 (16577) hydrogen bonds : bond 0.23821 ( 579) hydrogen bonds : angle 7.94672 ( 1659) *********************** 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 : 0.400 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: A 249 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7786 (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: 0.6673 (m-80) REVERT: A 1055 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6928 (tt) REVERT: A 1062 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7833 (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: 0.2835 time to fit residues: 105.0864 Evaluate side-chains 160 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.4960 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.144501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.107012 restraints weight = 57958.737| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.89 r_work: 0.3662 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12233 Z= 0.139 Angle : 0.586 5.587 16577 Z= 0.306 Chirality : 0.041 0.193 1890 Planarity : 0.005 0.040 2085 Dihedral : 8.676 78.237 1693 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.39 % Allowed : 10.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.22), residues: 1445 helix: 0.35 (0.20), residues: 674 sheet: -1.28 (0.33), residues: 235 loop : -0.77 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 531 TYR 0.012 0.001 TYR A 935 PHE 0.015 0.002 PHE A 696 TRP 0.012 0.001 TRP A1080 HIS 0.005 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00296 (12233) covalent geometry : angle 0.58586 (16577) hydrogen bonds : bond 0.06140 ( 579) hydrogen bonds : angle 5.43591 ( 1659) *********************** 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 177 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.574 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 125 TRP cc_start: 0.7655 (m-10) cc_final: 0.7220 (m-10) REVERT: A 249 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7977 (t80) REVERT: A 428 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8029 (mp) REVERT: A 547 MET cc_start: 0.7108 (ptp) cc_final: 0.6775 (ptp) REVERT: A 581 GLU cc_start: 0.5979 (tp30) cc_final: 0.5557 (mp0) REVERT: A 851 MET cc_start: 0.7285 (mtp) cc_final: 0.7036 (mtp) REVERT: A 903 LYS cc_start: 0.7335 (mttt) cc_final: 0.7112 (tptm) REVERT: A 993 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.6870 (m-80) REVERT: A 998 SER cc_start: 0.7750 (p) cc_final: 0.7457 (m) REVERT: A 1055 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7043 (tt) REVERT: B 239 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8996 (tt) REVERT: B 730 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6701 (p90) outliers start: 45 outliers final: 30 residues processed: 168 average time/residue: 0.2444 time to fit residues: 57.1253 Evaluate side-chains 140 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 259 MET Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 330 THR 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 535 ASN 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 35 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.142869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.107436 restraints weight = 57508.074| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.67 r_work: 0.3645 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12233 Z= 0.173 Angle : 0.561 6.791 16577 Z= 0.294 Chirality : 0.041 0.207 1890 Planarity : 0.004 0.042 2085 Dihedral : 7.642 89.820 1661 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.32 % Allowed : 10.63 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.22), residues: 1445 helix: 0.33 (0.20), residues: 683 sheet: -1.31 (0.33), residues: 235 loop : -0.87 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 700 TYR 0.019 0.002 TYR A 935 PHE 0.022 0.002 PHE A 696 TRP 0.013 0.001 TRP A1080 HIS 0.012 0.001 HIS A1089 Details of bonding type rmsd covalent geometry : bond 0.00398 (12233) covalent geometry : angle 0.56147 (16577) hydrogen bonds : bond 0.05250 ( 579) hydrogen bonds : angle 5.16371 ( 1659) *********************** 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 153 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 0.612 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 248 PHE cc_start: 0.7710 (t80) cc_final: 0.7473 (t80) REVERT: A 249 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7991 (t80) REVERT: A 306 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8793 (p) REVERT: A 428 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8087 (mp) REVERT: A 431 LEU cc_start: 0.8085 (mt) cc_final: 0.7566 (mt) REVERT: A 547 MET cc_start: 0.7134 (ptp) cc_final: 0.6846 (ptp) REVERT: A 581 GLU cc_start: 0.6060 (tp30) cc_final: 0.5615 (mp0) REVERT: A 903 LYS cc_start: 0.7378 (mttt) cc_final: 0.7143 (tptm) REVERT: A 993 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: A 998 SER cc_start: 0.7739 (p) cc_final: 0.7456 (m) REVERT: A 1055 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7108 (tt) REVERT: B 239 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8915 (tt) REVERT: B 730 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.6506 (p90) outliers start: 44 outliers final: 32 residues processed: 140 average time/residue: 0.2296 time to fit residues: 45.2146 Evaluate side-chains 143 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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 306 VAL 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 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 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 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 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 40 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.141651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.105283 restraints weight = 58814.364| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.87 r_work: 0.3618 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3112 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= 0.185 Angle : 0.555 6.873 16577 Z= 0.290 Chirality : 0.041 0.158 1890 Planarity : 0.004 0.047 2085 Dihedral : 7.294 75.131 1654 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.54 % Allowed : 11.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.22), residues: 1445 helix: 0.38 (0.20), residues: 677 sheet: -1.35 (0.33), residues: 235 loop : -1.06 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 700 TYR 0.020 0.002 TYR A 935 PHE 0.020 0.002 PHE A 696 TRP 0.011 0.001 TRP A1080 HIS 0.006 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00430 (12233) covalent geometry : angle 0.55538 (16577) hydrogen bonds : bond 0.04648 ( 579) hydrogen bonds : angle 4.99742 ( 1659) *********************** 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: 47 poor density : 104 time to evaluate : 0.573 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: 0.8502 (OUTLIER) cc_final: 0.8252 (t80) REVERT: A 428 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8115 (mp) REVERT: A 547 MET cc_start: 0.7150 (ptp) cc_final: 0.6862 (ptp) REVERT: A 581 GLU cc_start: 0.5990 (tp30) cc_final: 0.5549 (mp0) REVERT: A 993 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6920 (m-80) REVERT: A 998 SER cc_start: 0.7835 (p) cc_final: 0.7528 (m) REVERT: A 1033 MET cc_start: 0.7183 (mtt) cc_final: 0.6869 (mtp) REVERT: A 1055 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7022 (tt) REVERT: B 239 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8900 (tt) REVERT: B 730 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.6715 (p90) outliers start: 47 outliers final: 34 residues processed: 137 average time/residue: 0.2439 time to fit residues: 48.1406 Evaluate side-chains 140 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 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 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 135 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4284 r_free = 0.4284 target = 0.141258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.103833 restraints weight = 58603.792| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.82 r_work: 0.3615 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3303 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= 0.191 Angle : 0.555 7.237 16577 Z= 0.290 Chirality : 0.041 0.153 1890 Planarity : 0.004 0.051 2085 Dihedral : 7.224 64.439 1652 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.54 % Allowed : 11.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.22), residues: 1445 helix: 0.43 (0.20), residues: 675 sheet: -1.35 (0.33), residues: 235 loop : -1.19 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 700 TYR 0.020 0.002 TYR A 935 PHE 0.019 0.002 PHE A 696 TRP 0.010 0.001 TRP A1080 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00447 (12233) covalent geometry : angle 0.55452 (16577) hydrogen bonds : bond 0.04563 ( 579) hydrogen bonds : angle 4.93631 ( 1659) *********************** 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 149 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 102 time to evaluate : 0.515 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: A 249 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8339 (t80) REVERT: A 428 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 547 MET cc_start: 0.7149 (ptp) cc_final: 0.6864 (ptp) REVERT: A 581 GLU cc_start: 0.6026 (tp30) cc_final: 0.5567 (mp0) REVERT: A 717 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7050 (tp) REVERT: A 903 LYS cc_start: 0.8494 (tptm) cc_final: 0.8050 (tptp) REVERT: A 993 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: A 998 SER cc_start: 0.7902 (p) cc_final: 0.7571 (m) REVERT: A 1033 MET cc_start: 0.7259 (mtt) cc_final: 0.6937 (mtp) REVERT: A 1055 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7060 (tt) REVERT: B 239 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8893 (tt) REVERT: B 730 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6660 (p90) outliers start: 47 outliers final: 37 residues processed: 136 average time/residue: 0.2361 time to fit residues: 46.1267 Evaluate side-chains 140 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 96 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 236 SER 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 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 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 Chi-restraints excluded: chain B residue 809 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.143041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.105840 restraints weight = 58262.955| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.18 r_work: 0.3620 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12233 Z= 0.115 Angle : 0.497 5.694 16577 Z= 0.255 Chirality : 0.040 0.157 1890 Planarity : 0.004 0.056 2085 Dihedral : 7.000 58.704 1652 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.87 % Allowed : 12.14 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.22), residues: 1445 helix: 0.77 (0.20), residues: 679 sheet: -1.24 (0.34), residues: 238 loop : -0.98 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 531 TYR 0.018 0.001 TYR B 659 PHE 0.013 0.001 PHE A 696 TRP 0.011 0.001 TRP A1080 HIS 0.009 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00269 (12233) covalent geometry : angle 0.49724 (16577) hydrogen bonds : bond 0.03839 ( 579) hydrogen bonds : angle 4.61588 ( 1659) *********************** 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 140 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.420 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: A 249 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8276 (t80) REVERT: A 428 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 547 MET cc_start: 0.7041 (ptp) cc_final: 0.6775 (ptp) REVERT: A 581 GLU cc_start: 0.5857 (tp30) cc_final: 0.5477 (mp0) REVERT: A 903 LYS cc_start: 0.8480 (tptm) cc_final: 0.8038 (tptp) REVERT: A 993 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: A 998 SER cc_start: 0.7796 (p) cc_final: 0.7464 (m) REVERT: A 1055 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6845 (tt) REVERT: B 239 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8819 (tt) REVERT: B 730 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.6958 (p90) outliers start: 38 outliers final: 32 residues processed: 132 average time/residue: 0.2294 time to fit residues: 43.2081 Evaluate side-chains 132 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 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 239 LEU 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 657 LEU 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 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 80 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.142145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.104953 restraints weight = 58502.171| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.21 r_work: 0.3605 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12233 Z= 0.151 Angle : 0.512 6.402 16577 Z= 0.265 Chirality : 0.040 0.149 1890 Planarity : 0.004 0.055 2085 Dihedral : 6.884 59.569 1650 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.02 % Allowed : 12.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.22), residues: 1445 helix: 0.75 (0.20), residues: 679 sheet: -1.31 (0.33), residues: 235 loop : -1.02 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 531 TYR 0.017 0.001 TYR A 935 PHE 0.016 0.001 PHE A 696 TRP 0.009 0.001 TRP A1080 HIS 0.006 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00352 (12233) covalent geometry : angle 0.51226 (16577) hydrogen bonds : bond 0.03970 ( 579) hydrogen bonds : angle 4.66197 ( 1659) *********************** 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 136 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.578 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: A 428 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8028 (mp) REVERT: A 547 MET cc_start: 0.7024 (ptp) cc_final: 0.6763 (ptp) REVERT: A 581 GLU cc_start: 0.5872 (tp30) cc_final: 0.5456 (mp0) REVERT: A 717 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6873 (tp) REVERT: A 903 LYS cc_start: 0.8424 (tptm) cc_final: 0.8015 (tptp) REVERT: A 993 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: A 998 SER cc_start: 0.7819 (p) cc_final: 0.7491 (m) REVERT: A 1033 MET cc_start: 0.7108 (mtt) cc_final: 0.6827 (mtp) REVERT: A 1055 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6878 (tt) REVERT: B 239 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8841 (tt) REVERT: B 730 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.6921 (p90) outliers start: 40 outliers final: 32 residues processed: 126 average time/residue: 0.2186 time to fit residues: 40.5527 Evaluate side-chains 131 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 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 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 620 VAL Chi-restraints excluded: chain B residue 657 LEU 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 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 135 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.142029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.104220 restraints weight = 58339.208| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.90 r_work: 0.3622 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3612 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= 0.144 Angle : 0.507 6.277 16577 Z= 0.261 Chirality : 0.040 0.149 1890 Planarity : 0.004 0.065 2085 Dihedral : 6.794 58.565 1648 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.22), residues: 1445 helix: 0.83 (0.20), residues: 677 sheet: -1.31 (0.33), residues: 234 loop : -1.04 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 531 TYR 0.014 0.001 TYR A 935 PHE 0.016 0.001 PHE A 696 TRP 0.009 0.001 TRP A1080 HIS 0.007 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00336 (12233) covalent geometry : angle 0.50710 (16577) hydrogen bonds : bond 0.03860 ( 579) hydrogen bonds : angle 4.59186 ( 1659) *********************** 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 140 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.659 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: A 428 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8149 (mp) REVERT: A 547 MET cc_start: 0.7127 (ptp) cc_final: 0.6859 (ptp) REVERT: A 581 GLU cc_start: 0.5919 (tp30) cc_final: 0.5480 (mp0) REVERT: A 717 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6947 (tp) REVERT: A 903 LYS cc_start: 0.8459 (tptm) cc_final: 0.8046 (tptp) REVERT: A 993 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: A 998 SER cc_start: 0.7973 (p) cc_final: 0.7622 (m) REVERT: A 1033 MET cc_start: 0.7132 (mtt) cc_final: 0.6857 (mtp) REVERT: A 1055 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7053 (tt) REVERT: B 64 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8404 (mm-40) REVERT: B 239 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8872 (tt) REVERT: B 730 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.6990 (p90) outliers start: 43 outliers final: 33 residues processed: 130 average time/residue: 0.2579 time to fit residues: 48.7650 Evaluate side-chains 133 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 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 847 ILE 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 84 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 124 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.143401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.105616 restraints weight = 58227.477| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.93 r_work: 0.3644 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12233 Z= 0.099 Angle : 0.479 5.273 16577 Z= 0.243 Chirality : 0.039 0.153 1890 Planarity : 0.004 0.065 2085 Dihedral : 6.600 57.925 1648 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.56 % Allowed : 12.82 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.23), residues: 1445 helix: 1.14 (0.20), residues: 678 sheet: -1.18 (0.33), residues: 237 loop : -0.82 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 531 TYR 0.012 0.001 TYR B 659 PHE 0.011 0.001 PHE A 696 TRP 0.010 0.001 TRP A1080 HIS 0.009 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00227 (12233) covalent geometry : angle 0.47867 (16577) hydrogen bonds : bond 0.03434 ( 579) hydrogen bonds : angle 4.38330 ( 1659) *********************** 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 133 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.620 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: A 428 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8105 (mp) REVERT: A 547 MET cc_start: 0.7164 (ptp) cc_final: 0.6897 (ptp) REVERT: A 581 GLU cc_start: 0.5938 (tp30) cc_final: 0.5524 (mp0) REVERT: A 903 LYS cc_start: 0.8447 (tptm) cc_final: 0.8031 (tptp) REVERT: A 993 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.6870 (m-80) REVERT: A 998 SER cc_start: 0.7899 (p) cc_final: 0.7550 (m) REVERT: A 1055 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6987 (tt) REVERT: B 64 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8412 (mm-40) REVERT: B 239 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8855 (tt) REVERT: B 730 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7003 (p90) outliers start: 34 outliers final: 27 residues processed: 125 average time/residue: 0.2524 time to fit residues: 45.0170 Evaluate side-chains 128 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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 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 64 GLN Chi-restraints excluded: chain B residue 84 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 39 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 105 optimal weight: 0.0980 chunk 141 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.141538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.103699 restraints weight = 58360.933| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.92 r_work: 0.3616 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12233 Z= 0.158 Angle : 0.512 6.246 16577 Z= 0.263 Chirality : 0.040 0.146 1890 Planarity : 0.004 0.066 2085 Dihedral : 6.659 58.576 1647 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.41 % Allowed : 13.50 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.23), residues: 1445 helix: 0.97 (0.20), residues: 678 sheet: -1.26 (0.33), residues: 235 loop : -0.96 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 531 TYR 0.017 0.001 TYR A 935 PHE 0.017 0.001 PHE A 696 TRP 0.010 0.001 TRP A1080 HIS 0.005 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00371 (12233) covalent geometry : angle 0.51163 (16577) hydrogen bonds : bond 0.03770 ( 579) hydrogen bonds : angle 4.52914 ( 1659) ********************** 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 126 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.511 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: A 428 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8164 (mp) REVERT: A 547 MET cc_start: 0.7192 (ptp) cc_final: 0.6926 (ptp) REVERT: A 581 GLU cc_start: 0.5934 (tp30) cc_final: 0.5495 (mp0) REVERT: A 903 LYS cc_start: 0.8476 (tptm) cc_final: 0.8061 (tptp) REVERT: A 993 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.6897 (m-80) REVERT: A 998 SER cc_start: 0.8016 (p) cc_final: 0.7653 (m) REVERT: A 1033 MET cc_start: 0.7104 (mtt) cc_final: 0.6843 (mtp) REVERT: A 1055 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7057 (tt) REVERT: B 64 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8406 (mm-40) REVERT: B 239 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8892 (tt) REVERT: B 730 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7011 (p90) outliers start: 32 outliers final: 25 residues processed: 118 average time/residue: 0.2448 time to fit residues: 42.2846 Evaluate side-chains 124 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 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 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 64 GLN Chi-restraints excluded: chain B residue 84 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 137 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 136 optimal weight: 0.0270 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.142791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.104957 restraints weight = 58051.293| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.93 r_work: 0.3632 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12233 Z= 0.110 Angle : 0.479 5.476 16577 Z= 0.244 Chirality : 0.039 0.152 1890 Planarity : 0.004 0.053 2085 Dihedral : 6.455 59.201 1645 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.34 % Allowed : 13.57 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.23), residues: 1445 helix: 1.20 (0.20), residues: 678 sheet: -1.11 (0.33), residues: 231 loop : -0.81 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 947 TYR 0.012 0.001 TYR B 659 PHE 0.013 0.001 PHE A 696 TRP 0.009 0.001 TRP A1080 HIS 0.009 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00256 (12233) covalent geometry : angle 0.47933 (16577) hydrogen bonds : bond 0.03432 ( 579) hydrogen bonds : angle 4.35467 ( 1659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6074.09 seconds wall clock time: 103 minutes 31.75 seconds (6211.75 seconds total)