Starting phenix.real_space_refine on Wed May 14 20:35:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9y_36119/05_2025/8j9y_36119.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9y_36119/05_2025/8j9y_36119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j9y_36119/05_2025/8j9y_36119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9y_36119/05_2025/8j9y_36119.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9y_36119/05_2025/8j9y_36119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9y_36119/05_2025/8j9y_36119.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7818 2.51 5 N 2086 2.21 5 O 2200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12154 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6077 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 10.07, per 1000 atoms: 0.83 Number of scatterers: 12154 At special positions: 0 Unit cell: (114.95, 109.25, 111.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2200 8.00 N 2086 7.00 C 7818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 16 sheets defined 53.7% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.879A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.721A pdb=" N LYS B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.705A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.541A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 642 through 654 removed outlier: 4.062A pdb=" N LYS B 646 " --> pdb=" O ASP B 642 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU B 647 " --> pdb=" O ASP B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 664 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.748A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN B 706 " --> pdb=" O ALA B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 754 through 766 Processing helix chain 'B' and resid 806 through 814 removed outlier: 3.951A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 877 Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 942 through 953 removed outlier: 3.586A pdb=" N SER B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 982 through 990 Processing helix chain 'B' and resid 997 through 1004 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.571A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 3.513A pdb=" N LEU B1042 " --> pdb=" O TYR B1038 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR B1043 " --> pdb=" O ARG B1039 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B1045 " --> pdb=" O GLU B1041 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1092 Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1109 through 1117 Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'B' and resid 1129 through 1133 Processing helix chain 'B' and resid 1134 through 1160 Processing helix chain 'B' and resid 1166 through 1187 Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.878A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.721A pdb=" N LYS A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.705A pdb=" N HIS A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.540A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 642 through 654 removed outlier: 4.062A pdb=" N LYS A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.748A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 754 through 766 Processing helix chain 'A' and resid 806 through 814 removed outlier: 3.950A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.585A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 982 through 990 Processing helix chain 'A' and resid 997 through 1004 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.570A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 3.512A pdb=" N LEU A1042 " --> pdb=" O TYR A1038 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A1043 " --> pdb=" O ARG A1039 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A1045 " --> pdb=" O GLU A1041 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 Processing helix chain 'A' and resid 1081 through 1092 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1117 Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1129 through 1133 Processing helix chain 'A' and resid 1134 through 1160 Processing helix chain 'A' and resid 1166 through 1187 Processing sheet with id=AA1, first strand: chain 'B' and resid 418 through 419 removed outlier: 6.358A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.181A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 849 through 852 Processing sheet with id=AA6, first strand: chain 'B' and resid 910 through 913 Processing sheet with id=AA7, first strand: chain 'B' and resid 922 through 926 removed outlier: 6.250A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 975 " --> pdb=" O ILE B 963 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B 963 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 977 " --> pdb=" O GLU B 961 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1013 through 1016 removed outlier: 4.320A pdb=" N LEU B1013 " --> pdb=" O PHE B1025 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 418 through 419 removed outlier: 6.358A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AB2, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AB3, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.181A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 849 through 852 Processing sheet with id=AB5, first strand: chain 'A' and resid 910 through 913 Processing sheet with id=AB6, first strand: chain 'A' and resid 922 through 926 removed outlier: 6.251A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 975 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A 963 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS A 977 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1013 through 1016 removed outlier: 4.321A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1704 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: 4.26 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3910 1.34 - 1.46: 2690 1.46 - 1.58: 5768 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12446 Sorted by residual: bond pdb=" CB PRO A 881 " pdb=" CG PRO A 881 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.68e+00 bond pdb=" CB PRO B 881 " pdb=" CG PRO B 881 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.68e+00 bond pdb=" C ILE B 896 " pdb=" N LEU B 897 " ideal model delta sigma weight residual 1.331 1.354 -0.023 2.07e-02 2.33e+03 1.20e+00 bond pdb=" C ILE A 896 " pdb=" N LEU A 897 " ideal model delta sigma weight residual 1.331 1.353 -0.022 2.07e-02 2.33e+03 1.17e+00 bond pdb=" N LYS A 882 " pdb=" CA LYS A 882 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.52e-01 ... (remaining 12441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 16502 1.45 - 2.90: 246 2.90 - 4.34: 54 4.34 - 5.79: 10 5.79 - 7.24: 4 Bond angle restraints: 16816 Sorted by residual: angle pdb=" N ASN B 930 " pdb=" CA ASN B 930 " pdb=" C ASN B 930 " ideal model delta sigma weight residual 111.02 107.36 3.66 1.25e+00 6.40e-01 8.59e+00 angle pdb=" N ASN A 930 " pdb=" CA ASN A 930 " pdb=" C ASN A 930 " ideal model delta sigma weight residual 111.02 107.39 3.63 1.25e+00 6.40e-01 8.41e+00 angle pdb=" C HIS A 631 " pdb=" N PHE A 632 " pdb=" CA PHE A 632 " ideal model delta sigma weight residual 120.82 124.91 -4.09 1.50e+00 4.44e-01 7.42e+00 angle pdb=" C SER A 455 " pdb=" N ASN A 456 " pdb=" CA ASN A 456 " ideal model delta sigma weight residual 121.80 126.86 -5.06 2.44e+00 1.68e-01 4.31e+00 angle pdb=" CA LEU A 452 " pdb=" CB LEU A 452 " pdb=" CG LEU A 452 " ideal model delta sigma weight residual 116.30 123.54 -7.24 3.50e+00 8.16e-02 4.28e+00 ... (remaining 16811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 6496 16.96 - 33.91: 738 33.91 - 50.87: 210 50.87 - 67.82: 24 67.82 - 84.78: 6 Dihedral angle restraints: 7474 sinusoidal: 3088 harmonic: 4386 Sorted by residual: dihedral pdb=" CG ARG A 873 " pdb=" CD ARG A 873 " pdb=" NE ARG A 873 " pdb=" CZ ARG A 873 " ideal model delta sinusoidal sigma weight residual 180.00 137.17 42.83 2 1.50e+01 4.44e-03 9.86e+00 dihedral pdb=" CG ARG B 873 " pdb=" CD ARG B 873 " pdb=" NE ARG B 873 " pdb=" CZ ARG B 873 " ideal model delta sinusoidal sigma weight residual 180.00 137.18 42.82 2 1.50e+01 4.44e-03 9.86e+00 dihedral pdb=" CA GLY A 453 " pdb=" C GLY A 453 " pdb=" N LYS A 454 " pdb=" CA LYS A 454 " ideal model delta harmonic sigma weight residual 180.00 164.39 15.61 0 5.00e+00 4.00e-02 9.75e+00 ... (remaining 7471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1066 0.025 - 0.049: 432 0.049 - 0.074: 212 0.074 - 0.099: 57 0.099 - 0.124: 53 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CA ILE B 685 " pdb=" N ILE B 685 " pdb=" C ILE B 685 " pdb=" CB ILE B 685 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA ILE A 685 " pdb=" N ILE A 685 " pdb=" C ILE A 685 " pdb=" CB ILE A 685 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA ILE B 963 " pdb=" N ILE B 963 " pdb=" C ILE B 963 " pdb=" CB ILE B 963 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 1817 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 880 " -0.051 5.00e-02 4.00e+02 7.64e-02 9.34e+00 pdb=" N PRO A 881 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 881 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 881 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 880 " 0.051 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO B 881 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 881 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 881 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 930 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C ASN B 930 " 0.028 2.00e-02 2.50e+03 pdb=" O ASN B 930 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 931 " -0.009 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 254 2.71 - 3.26: 11750 3.26 - 3.81: 19267 3.81 - 4.35: 24778 4.35 - 4.90: 42209 Nonbonded interactions: 98258 Sorted by model distance: nonbonded pdb=" O LYS A 979 " pdb=" OG SER A 982 " model vdw 2.167 3.040 nonbonded pdb=" O LYS B 979 " pdb=" OG SER B 982 " model vdw 2.169 3.040 nonbonded pdb=" O VAL B 838 " pdb=" NH2 ARG B1039 " model vdw 2.205 3.120 nonbonded pdb=" O VAL A 838 " pdb=" NH2 ARG A1039 " model vdw 2.205 3.120 nonbonded pdb=" OD1 ASP A 997 " pdb=" N SER A 998 " model vdw 2.226 3.120 ... (remaining 98253 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.330 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.002 0.065 12446 Z= 0.107 Angle : 0.498 7.241 16816 Z= 0.275 Chirality : 0.037 0.124 1820 Planarity : 0.004 0.076 2142 Dihedral : 15.113 84.780 4662 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.76 % Allowed : 11.91 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1486 helix: 1.47 (0.19), residues: 680 sheet: -0.64 (0.38), residues: 212 loop : -0.31 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1189 HIS 0.005 0.001 HIS A 650 PHE 0.007 0.001 PHE B 629 TYR 0.008 0.001 TYR A1079 ARG 0.007 0.000 ARG A1004 Details of bonding type rmsd hydrogen bonds : bond 0.15837 ( 598) hydrogen bonds : angle 6.51956 ( 1704) covalent geometry : bond 0.00225 (12446) covalent geometry : angle 0.49814 (16816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 1.231 Fit side-chains REVERT: B 663 GLU cc_start: 0.6940 (tp30) cc_final: 0.6522 (tp30) REVERT: A 663 GLU cc_start: 0.6923 (tp30) cc_final: 0.6504 (tp30) outliers start: 10 outliers final: 2 residues processed: 146 average time/residue: 0.2627 time to fit residues: 54.0336 Evaluate side-chains 135 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain A residue 982 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 623 HIS B 887 HIS B 892 HIS A 623 HIS A 887 HIS A 892 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.148413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.111833 restraints weight = 13354.960| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.01 r_work: 0.2883 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12446 Z= 0.131 Angle : 0.499 8.274 16816 Z= 0.257 Chirality : 0.039 0.141 1820 Planarity : 0.004 0.052 2142 Dihedral : 3.614 16.451 1664 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.53 % Allowed : 12.14 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.22), residues: 1486 helix: 1.77 (0.19), residues: 704 sheet: -0.54 (0.38), residues: 216 loop : -0.25 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.003 0.001 HIS A1051 PHE 0.009 0.001 PHE A 739 TYR 0.011 0.001 TYR B 837 ARG 0.005 0.001 ARG B1004 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 598) hydrogen bonds : angle 4.76277 ( 1704) covalent geometry : bond 0.00311 (12446) covalent geometry : angle 0.49934 (16816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.272 Fit side-chains REVERT: B 851 ASN cc_start: 0.6620 (m-40) cc_final: 0.6382 (m-40) REVERT: B 997 ASP cc_start: 0.7693 (t0) cc_final: 0.7279 (t0) REVERT: B 1019 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7962 (pptt) REVERT: B 1080 GLU cc_start: 0.7901 (tt0) cc_final: 0.7247 (tp30) REVERT: A 851 ASN cc_start: 0.6645 (m-40) cc_final: 0.6424 (m-40) REVERT: A 997 ASP cc_start: 0.7713 (t0) cc_final: 0.7300 (t0) REVERT: A 1019 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7963 (pptt) REVERT: A 1080 GLU cc_start: 0.7909 (tt0) cc_final: 0.7275 (tp30) outliers start: 20 outliers final: 14 residues processed: 150 average time/residue: 0.2499 time to fit residues: 53.6756 Evaluate side-chains 139 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 634 ASN Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1019 LYS Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.144719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.106715 restraints weight = 13688.068| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.51 r_work: 0.2775 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12446 Z= 0.169 Angle : 0.517 7.962 16816 Z= 0.267 Chirality : 0.041 0.147 1820 Planarity : 0.004 0.051 2142 Dihedral : 3.797 15.567 1662 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.98 % Allowed : 12.82 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.22), residues: 1486 helix: 1.85 (0.19), residues: 692 sheet: -0.58 (0.37), residues: 228 loop : -0.29 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1189 HIS 0.005 0.001 HIS B 623 PHE 0.011 0.001 PHE B1191 TYR 0.012 0.002 TYR A 920 ARG 0.004 0.000 ARG B1004 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 598) hydrogen bonds : angle 4.56818 ( 1704) covalent geometry : bond 0.00415 (12446) covalent geometry : angle 0.51720 (16816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.578 Fit side-chains REVERT: B 851 ASN cc_start: 0.6759 (m-40) cc_final: 0.6476 (m-40) REVERT: B 997 ASP cc_start: 0.7750 (t0) cc_final: 0.7231 (t0) REVERT: B 1019 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7856 (pptt) REVERT: B 1046 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7011 (ttt180) REVERT: B 1073 GLU cc_start: 0.8045 (tt0) cc_final: 0.7634 (mt-10) REVERT: B 1080 GLU cc_start: 0.7801 (tt0) cc_final: 0.7163 (tp30) REVERT: A 851 ASN cc_start: 0.6754 (m-40) cc_final: 0.6485 (m-40) REVERT: A 997 ASP cc_start: 0.7760 (t0) cc_final: 0.7242 (t0) REVERT: A 1019 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7858 (pptt) REVERT: A 1046 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7024 (ttt180) REVERT: A 1073 GLU cc_start: 0.8060 (tt0) cc_final: 0.7625 (mt-10) REVERT: A 1080 GLU cc_start: 0.7755 (tt0) cc_final: 0.7125 (tp30) outliers start: 26 outliers final: 14 residues processed: 162 average time/residue: 0.2754 time to fit residues: 62.8930 Evaluate side-chains 142 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 1019 LYS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 17 optimal weight: 0.0030 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 0.0470 chunk 39 optimal weight: 0.5980 chunk 127 optimal weight: 0.0370 overall best weight: 0.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.150276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.112080 restraints weight = 13172.218| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.08 r_work: 0.2994 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12446 Z= 0.085 Angle : 0.430 6.911 16816 Z= 0.224 Chirality : 0.038 0.139 1820 Planarity : 0.003 0.047 2142 Dihedral : 3.463 16.369 1662 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.15 % Allowed : 13.74 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.23), residues: 1486 helix: 2.16 (0.20), residues: 692 sheet: -0.39 (0.39), residues: 216 loop : -0.21 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1189 HIS 0.005 0.000 HIS B 609 PHE 0.012 0.001 PHE A 959 TYR 0.009 0.001 TYR A 920 ARG 0.003 0.000 ARG A1004 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 598) hydrogen bonds : angle 4.15194 ( 1704) covalent geometry : bond 0.00180 (12446) covalent geometry : angle 0.42984 (16816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 851 ASN cc_start: 0.6671 (m-40) cc_final: 0.6363 (m-40) REVERT: B 997 ASP cc_start: 0.7820 (t0) cc_final: 0.7278 (t0) REVERT: B 1019 LYS cc_start: 0.8149 (mttp) cc_final: 0.7846 (pptt) REVERT: B 1073 GLU cc_start: 0.8165 (tt0) cc_final: 0.7631 (mt-10) REVERT: B 1080 GLU cc_start: 0.7878 (tt0) cc_final: 0.7283 (tp30) REVERT: A 851 ASN cc_start: 0.6673 (m-40) cc_final: 0.6362 (m-40) REVERT: A 997 ASP cc_start: 0.7843 (t0) cc_final: 0.7306 (t0) REVERT: A 1019 LYS cc_start: 0.8153 (mttp) cc_final: 0.7831 (pptt) REVERT: A 1073 GLU cc_start: 0.8164 (tt0) cc_final: 0.7639 (mt-10) REVERT: A 1080 GLU cc_start: 0.7856 (tt0) cc_final: 0.7267 (tp30) outliers start: 15 outliers final: 15 residues processed: 150 average time/residue: 0.2733 time to fit residues: 57.3929 Evaluate side-chains 139 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1046 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 125 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.146278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.108162 restraints weight = 13338.216| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.49 r_work: 0.2854 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12446 Z= 0.139 Angle : 0.471 7.552 16816 Z= 0.244 Chirality : 0.039 0.140 1820 Planarity : 0.003 0.052 2142 Dihedral : 3.604 15.522 1662 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.76 % Allowed : 13.97 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.23), residues: 1486 helix: 2.09 (0.19), residues: 704 sheet: -0.49 (0.37), residues: 228 loop : -0.18 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1189 HIS 0.005 0.001 HIS B 609 PHE 0.010 0.001 PHE B 596 TYR 0.010 0.001 TYR B 920 ARG 0.003 0.000 ARG B1057 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 598) hydrogen bonds : angle 4.23915 ( 1704) covalent geometry : bond 0.00340 (12446) covalent geometry : angle 0.47087 (16816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.268 Fit side-chains REVERT: B 851 ASN cc_start: 0.6670 (m-40) cc_final: 0.6422 (m110) REVERT: B 997 ASP cc_start: 0.7786 (t0) cc_final: 0.7215 (t0) REVERT: B 1019 LYS cc_start: 0.8058 (mttp) cc_final: 0.7810 (pptt) REVERT: B 1046 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.6984 (ttt180) REVERT: B 1073 GLU cc_start: 0.8165 (tt0) cc_final: 0.7627 (mt-10) REVERT: B 1080 GLU cc_start: 0.7762 (tt0) cc_final: 0.7189 (tp30) REVERT: A 851 ASN cc_start: 0.6666 (m-40) cc_final: 0.6433 (m110) REVERT: A 997 ASP cc_start: 0.7803 (t0) cc_final: 0.7231 (t0) REVERT: A 1019 LYS cc_start: 0.8059 (mttp) cc_final: 0.7802 (pptt) REVERT: A 1046 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.6952 (ttt180) REVERT: A 1073 GLU cc_start: 0.8183 (tt0) cc_final: 0.7640 (mt-10) REVERT: A 1080 GLU cc_start: 0.7766 (tt0) cc_final: 0.7187 (tp30) outliers start: 23 outliers final: 16 residues processed: 152 average time/residue: 0.2482 time to fit residues: 54.5669 Evaluate side-chains 144 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 11 optimal weight: 5.9990 chunk 113 optimal weight: 0.0870 chunk 24 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 ASN B 892 HIS A 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.143868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.104843 restraints weight = 13715.772| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.40 r_work: 0.2802 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12446 Z= 0.213 Angle : 0.538 8.316 16816 Z= 0.279 Chirality : 0.042 0.143 1820 Planarity : 0.004 0.054 2142 Dihedral : 3.911 16.034 1662 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.76 % Allowed : 13.82 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.22), residues: 1486 helix: 1.90 (0.19), residues: 702 sheet: -0.73 (0.37), residues: 228 loop : -0.30 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1189 HIS 0.004 0.001 HIS A1051 PHE 0.015 0.002 PHE B1191 TYR 0.013 0.002 TYR B 591 ARG 0.003 0.000 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 598) hydrogen bonds : angle 4.45800 ( 1704) covalent geometry : bond 0.00533 (12446) covalent geometry : angle 0.53801 (16816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.277 Fit side-chains REVERT: B 928 GLN cc_start: 0.8135 (mp10) cc_final: 0.7818 (mp10) REVERT: B 997 ASP cc_start: 0.7833 (t0) cc_final: 0.7240 (t0) REVERT: B 1019 LYS cc_start: 0.8102 (mttp) cc_final: 0.7838 (pptt) REVERT: B 1046 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7015 (ttt180) REVERT: B 1073 GLU cc_start: 0.8154 (tt0) cc_final: 0.7895 (tt0) REVERT: B 1080 GLU cc_start: 0.7733 (tt0) cc_final: 0.7254 (tp30) REVERT: A 928 GLN cc_start: 0.8155 (mp10) cc_final: 0.7857 (mp10) REVERT: A 930 ASN cc_start: 0.8261 (t0) cc_final: 0.7692 (t0) REVERT: A 997 ASP cc_start: 0.7841 (t0) cc_final: 0.7248 (t0) REVERT: A 1019 LYS cc_start: 0.8099 (mttp) cc_final: 0.7837 (pptt) REVERT: A 1046 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7037 (ttt180) REVERT: A 1073 GLU cc_start: 0.8162 (tt0) cc_final: 0.7907 (tt0) REVERT: A 1080 GLU cc_start: 0.7700 (tt0) cc_final: 0.7234 (tp30) outliers start: 23 outliers final: 16 residues processed: 146 average time/residue: 0.2702 time to fit residues: 56.4459 Evaluate side-chains 143 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 130 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.145445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.106468 restraints weight = 13548.995| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.24 r_work: 0.2811 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12446 Z= 0.147 Angle : 0.485 7.672 16816 Z= 0.252 Chirality : 0.040 0.141 1820 Planarity : 0.004 0.054 2142 Dihedral : 3.766 15.276 1662 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.53 % Allowed : 14.50 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1486 helix: 1.98 (0.19), residues: 702 sheet: -0.79 (0.37), residues: 228 loop : -0.26 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1189 HIS 0.004 0.001 HIS B 609 PHE 0.015 0.001 PHE B 959 TYR 0.010 0.001 TYR A 920 ARG 0.006 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 598) hydrogen bonds : angle 4.32715 ( 1704) covalent geometry : bond 0.00358 (12446) covalent geometry : angle 0.48485 (16816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.521 Fit side-chains REVERT: B 928 GLN cc_start: 0.8153 (mp10) cc_final: 0.7869 (mp10) REVERT: B 930 ASN cc_start: 0.8249 (t0) cc_final: 0.7643 (t0) REVERT: B 997 ASP cc_start: 0.7805 (t0) cc_final: 0.7194 (t0) REVERT: B 1019 LYS cc_start: 0.8180 (mttp) cc_final: 0.7841 (pptt) REVERT: B 1046 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7092 (ttt180) REVERT: B 1073 GLU cc_start: 0.8249 (tt0) cc_final: 0.8001 (tt0) REVERT: B 1080 GLU cc_start: 0.7783 (tt0) cc_final: 0.7245 (tp30) REVERT: A 420 ARG cc_start: 0.7872 (ptm160) cc_final: 0.7308 (ptm-80) REVERT: A 928 GLN cc_start: 0.8168 (mp10) cc_final: 0.7885 (mp10) REVERT: A 930 ASN cc_start: 0.8261 (t0) cc_final: 0.7663 (t0) REVERT: A 997 ASP cc_start: 0.7827 (t0) cc_final: 0.7216 (t0) REVERT: A 1019 LYS cc_start: 0.8175 (mttp) cc_final: 0.7840 (pptt) REVERT: A 1046 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7113 (ttt180) REVERT: A 1073 GLU cc_start: 0.8270 (tt0) cc_final: 0.8026 (tt0) REVERT: A 1080 GLU cc_start: 0.7766 (tt0) cc_final: 0.7232 (tp30) outliers start: 20 outliers final: 18 residues processed: 156 average time/residue: 0.2601 time to fit residues: 57.7886 Evaluate side-chains 149 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 64 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.147097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108898 restraints weight = 13609.415| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.26 r_work: 0.2861 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12446 Z= 0.111 Angle : 0.455 7.479 16816 Z= 0.237 Chirality : 0.038 0.140 1820 Planarity : 0.003 0.055 2142 Dihedral : 3.623 15.197 1662 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.76 % Allowed : 14.43 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1486 helix: 2.09 (0.20), residues: 704 sheet: -0.75 (0.37), residues: 228 loop : -0.22 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1189 HIS 0.006 0.001 HIS B 566 PHE 0.015 0.001 PHE B 959 TYR 0.012 0.001 TYR A 580 ARG 0.007 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 598) hydrogen bonds : angle 4.17707 ( 1704) covalent geometry : bond 0.00259 (12446) covalent geometry : angle 0.45531 (16816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.303 Fit side-chains REVERT: B 652 TYR cc_start: 0.8260 (m-80) cc_final: 0.7867 (m-80) REVERT: B 851 ASN cc_start: 0.6745 (m-40) cc_final: 0.6359 (m110) REVERT: B 928 GLN cc_start: 0.8139 (mp10) cc_final: 0.7857 (mp10) REVERT: B 997 ASP cc_start: 0.7740 (t0) cc_final: 0.7136 (t0) REVERT: B 1019 LYS cc_start: 0.8171 (mttp) cc_final: 0.7801 (pptt) REVERT: B 1046 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7052 (ttt180) REVERT: B 1073 GLU cc_start: 0.8236 (tt0) cc_final: 0.7996 (tt0) REVERT: B 1080 GLU cc_start: 0.7782 (tt0) cc_final: 0.7229 (tp30) REVERT: A 420 ARG cc_start: 0.7874 (ptm160) cc_final: 0.7294 (ptm-80) REVERT: A 652 TYR cc_start: 0.8250 (m-80) cc_final: 0.7858 (m-80) REVERT: A 928 GLN cc_start: 0.8161 (mp10) cc_final: 0.7882 (mp10) REVERT: A 930 ASN cc_start: 0.8242 (t0) cc_final: 0.7610 (t0) REVERT: A 997 ASP cc_start: 0.7781 (t0) cc_final: 0.7164 (t0) REVERT: A 1019 LYS cc_start: 0.8173 (mttp) cc_final: 0.7799 (pptt) REVERT: A 1046 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7072 (ttt180) REVERT: A 1073 GLU cc_start: 0.8246 (tt0) cc_final: 0.8010 (tt0) REVERT: A 1080 GLU cc_start: 0.7776 (tt0) cc_final: 0.7217 (tp30) outliers start: 23 outliers final: 21 residues processed: 159 average time/residue: 0.2693 time to fit residues: 60.2613 Evaluate side-chains 155 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.0670 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS B 930 ASN A 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.147163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.108341 restraints weight = 13475.265| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.14 r_work: 0.2849 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12446 Z= 0.112 Angle : 0.454 7.484 16816 Z= 0.236 Chirality : 0.038 0.140 1820 Planarity : 0.004 0.056 2142 Dihedral : 3.567 14.223 1662 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.91 % Allowed : 14.20 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.23), residues: 1486 helix: 2.13 (0.19), residues: 704 sheet: -0.80 (0.37), residues: 230 loop : -0.18 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1189 HIS 0.003 0.001 HIS A 609 PHE 0.014 0.001 PHE B 959 TYR 0.015 0.001 TYR B 580 ARG 0.005 0.000 ARG B1057 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 598) hydrogen bonds : angle 4.14416 ( 1704) covalent geometry : bond 0.00264 (12446) covalent geometry : angle 0.45417 (16816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.226 Fit side-chains REVERT: B 420 ARG cc_start: 0.7932 (ptm160) cc_final: 0.7409 (ptm-80) REVERT: B 851 ASN cc_start: 0.6691 (m-40) cc_final: 0.6324 (m110) REVERT: B 928 GLN cc_start: 0.8113 (mp10) cc_final: 0.7833 (mp10) REVERT: B 997 ASP cc_start: 0.7786 (t0) cc_final: 0.7183 (t0) REVERT: B 1019 LYS cc_start: 0.8185 (mttp) cc_final: 0.7843 (pptt) REVERT: B 1046 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7031 (ttt180) REVERT: B 1073 GLU cc_start: 0.8223 (tt0) cc_final: 0.7984 (tt0) REVERT: B 1080 GLU cc_start: 0.7764 (tt0) cc_final: 0.7248 (tp30) REVERT: A 851 ASN cc_start: 0.6755 (m-40) cc_final: 0.6397 (m110) REVERT: A 928 GLN cc_start: 0.8137 (mp10) cc_final: 0.7867 (mp10) REVERT: A 930 ASN cc_start: 0.8274 (t0) cc_final: 0.7633 (t0) REVERT: A 997 ASP cc_start: 0.7795 (t0) cc_final: 0.7187 (t0) REVERT: A 1019 LYS cc_start: 0.8182 (mttp) cc_final: 0.7847 (pptt) REVERT: A 1046 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7046 (ttt180) REVERT: A 1073 GLU cc_start: 0.8259 (tt0) cc_final: 0.8022 (tt0) REVERT: A 1080 GLU cc_start: 0.7766 (tt0) cc_final: 0.7234 (tp30) outliers start: 25 outliers final: 21 residues processed: 161 average time/residue: 0.2493 time to fit residues: 56.6574 Evaluate side-chains 152 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS B 930 ASN A 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.145616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.107066 restraints weight = 13522.511| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.30 r_work: 0.2808 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12446 Z= 0.153 Angle : 0.488 7.805 16816 Z= 0.254 Chirality : 0.040 0.141 1820 Planarity : 0.004 0.056 2142 Dihedral : 3.694 14.885 1662 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.83 % Allowed : 14.50 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1486 helix: 2.03 (0.19), residues: 704 sheet: -0.79 (0.37), residues: 228 loop : -0.22 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1189 HIS 0.007 0.001 HIS A 566 PHE 0.014 0.001 PHE B 959 TYR 0.015 0.001 TYR B 580 ARG 0.005 0.000 ARG B1004 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 598) hydrogen bonds : angle 4.24929 ( 1704) covalent geometry : bond 0.00375 (12446) covalent geometry : angle 0.48814 (16816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.258 Fit side-chains REVERT: B 420 ARG cc_start: 0.8004 (ptm160) cc_final: 0.7457 (ptm-80) REVERT: B 851 ASN cc_start: 0.6805 (m-40) cc_final: 0.6423 (m110) REVERT: B 928 GLN cc_start: 0.8108 (mp10) cc_final: 0.7826 (mp10) REVERT: B 997 ASP cc_start: 0.7808 (t0) cc_final: 0.7184 (t0) REVERT: B 1019 LYS cc_start: 0.8185 (mttp) cc_final: 0.7825 (pptt) REVERT: B 1046 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7124 (ttt180) REVERT: B 1073 GLU cc_start: 0.8241 (tt0) cc_final: 0.7991 (tt0) REVERT: B 1080 GLU cc_start: 0.7808 (tt0) cc_final: 0.7267 (tp30) REVERT: A 428 ARG cc_start: 0.7528 (mtp85) cc_final: 0.7210 (mtp-110) REVERT: A 928 GLN cc_start: 0.8140 (mp10) cc_final: 0.7866 (mp10) REVERT: A 930 ASN cc_start: 0.8264 (t0) cc_final: 0.7610 (t0) REVERT: A 997 ASP cc_start: 0.7812 (t0) cc_final: 0.7207 (t0) REVERT: A 1019 LYS cc_start: 0.8187 (mttp) cc_final: 0.7833 (pptt) REVERT: A 1046 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7140 (ttt180) REVERT: A 1073 GLU cc_start: 0.8259 (tt0) cc_final: 0.8013 (tt0) REVERT: A 1080 GLU cc_start: 0.7807 (tt0) cc_final: 0.7261 (tp30) outliers start: 24 outliers final: 22 residues processed: 152 average time/residue: 0.2612 time to fit residues: 56.5744 Evaluate side-chains 151 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS B 930 ASN A 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.146407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.107560 restraints weight = 13538.400| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.29 r_work: 0.2850 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12446 Z= 0.128 Angle : 0.469 7.705 16816 Z= 0.244 Chirality : 0.039 0.141 1820 Planarity : 0.004 0.055 2142 Dihedral : 3.635 14.732 1662 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.91 % Allowed : 14.27 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1486 helix: 2.06 (0.19), residues: 704 sheet: -0.78 (0.37), residues: 228 loop : -0.21 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1189 HIS 0.004 0.001 HIS B1192 PHE 0.016 0.001 PHE B 959 TYR 0.014 0.001 TYR B 580 ARG 0.005 0.000 ARG B1004 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 598) hydrogen bonds : angle 4.19167 ( 1704) covalent geometry : bond 0.00308 (12446) covalent geometry : angle 0.46936 (16816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6397.03 seconds wall clock time: 112 minutes 15.31 seconds (6735.31 seconds total)