Starting phenix.real_space_refine on Fri Jul 3 10:49:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7trf_26088/07_2026/7trf_26088.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trf_26088/07_2026/7trf_26088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7trf_26088/07_2026/7trf_26088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trf_26088/07_2026/7trf_26088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7trf_26088/07_2026/7trf_26088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trf_26088/07_2026/7trf_26088.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7trf_26088/07_2026/7trf_26088.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7trf_26088/07_2026/7trf_26088.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 224 5.49 5 S 38 5.16 5 C 7774 2.51 5 N 2469 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13581 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 642 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "B" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 4605 Classifications: {'RNA': 217} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 21, 'rna3p_pur': 85, 'rna3p_pyr': 96} Link IDs: {'rna2p': 36, 'rna3p': 180} Chain breaks: 2 Chain: "A" Number of atoms: 7488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7488 Classifications: {'peptide': 934} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 877} Chain breaks: 4 Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 2.07, per 1000 atoms: 0.15 Number of scatterers: 13581 At special positions: 0 Unit cell: (117.7, 122.1, 121, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 224 15.00 O 3076 8.00 N 2469 7.00 C 7774 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: 0.86 Conformation dependent library (CDL) restraints added in 407.6 milliseconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 59.4% alpha, 13.0% beta 64 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'F' and resid 38 through 50 removed outlier: 3.800A pdb=" N TYR F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN F 48 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL F 49 " --> pdb=" O VAL F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 86 removed outlier: 4.107A pdb=" N SER F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE F 66 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL F 67 " --> pdb=" O MET F 63 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE F 70 " --> pdb=" O PHE F 66 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 103 removed outlier: 4.193A pdb=" N ILE F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 124 removed outlier: 3.548A pdb=" N LYS F 109 " --> pdb=" O GLY F 105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 Processing helix chain 'E' and resid 27 through 38 removed outlier: 3.854A pdb=" N GLY E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 74 removed outlier: 4.561A pdb=" N VAL E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 64 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 91 removed outlier: 3.810A pdb=" N ALA E 87 " --> pdb=" O HIS E 83 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 98 removed outlier: 3.596A pdb=" N LEU E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.839A pdb=" N LEU A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 removed outlier: 4.000A pdb=" N LEU A 332 " --> pdb=" O LYS A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 366 removed outlier: 3.574A pdb=" N ALA A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 401 removed outlier: 4.037A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.782A pdb=" N LEU A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 454 removed outlier: 3.781A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.717A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.506A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.654A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 560 removed outlier: 3.764A pdb=" N HIS A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 4.388A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.515A pdb=" N GLU A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 672 removed outlier: 3.532A pdb=" N SER A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.652A pdb=" N LEU A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.762A pdb=" N ILE A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 765 through 769 removed outlier: 4.005A pdb=" N LEU A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 removed outlier: 3.583A pdb=" N PHE A 776 " --> pdb=" O TYR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 Processing helix chain 'A' and resid 837 through 854 Processing helix chain 'A' and resid 876 through 890 Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.788A pdb=" N ALA A 950 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 958 removed outlier: 4.052A pdb=" N LEU A 958 " --> pdb=" O ARG A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 Processing helix chain 'A' and resid 1024 through 1027 Processing helix chain 'A' and resid 1028 through 1051 removed outlier: 4.120A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A1051 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1082 removed outlier: 4.323A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TRP A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.651A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.508A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.712A pdb=" N ALA A1119 " --> pdb=" O LEU A1115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 89 through 90 removed outlier: 3.756A pdb=" N ILE F 90 " --> pdb=" O ARG E 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.418A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 160 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 168 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.579A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 744 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.418A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 160 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 168 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.579A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA6, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA7, first strand: chain 'A' and resid 598 through 600 removed outlier: 6.601A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 862 through 865 removed outlier: 3.640A pdb=" N VAL A 904 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 712 " --> pdb=" O LYS A 902 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS A 902 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 927 through 930 467 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 173 hydrogen bonds 330 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3548 1.34 - 1.46: 4450 1.46 - 1.58: 5835 1.58 - 1.71: 444 1.71 - 1.83: 51 Bond restraints: 14328 Sorted by residual: bond pdb=" C LYS A 973 " pdb=" N LEU A 974 " ideal model delta sigma weight residual 1.334 1.384 -0.049 1.27e-02 6.20e+03 1.50e+01 bond pdb=" CA ILE E 79 " pdb=" CB ILE E 79 " ideal model delta sigma weight residual 1.540 1.575 -0.035 1.10e-02 8.26e+03 1.04e+01 bond pdb=" N VAL E 31 " pdb=" CA VAL E 31 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.83e+00 bond pdb=" N ILE E 79 " pdb=" CA ILE E 79 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.32e-02 5.74e+03 9.48e+00 bond pdb=" N VAL A 697 " pdb=" CA VAL A 697 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.98e+00 ... (remaining 14323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 19306 1.52 - 3.05: 1007 3.05 - 4.57: 141 4.57 - 6.09: 19 6.09 - 7.61: 3 Bond angle restraints: 20476 Sorted by residual: angle pdb=" O LYS A 973 " pdb=" C LYS A 973 " pdb=" N LEU A 974 " ideal model delta sigma weight residual 122.07 117.21 4.86 1.03e+00 9.43e-01 2.23e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT D 12 " pdb=" C4 DT D 12 " pdb=" O4 DT D 12 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N VAL A 596 " pdb=" CA VAL A 596 " pdb=" C VAL A 596 " ideal model delta sigma weight residual 112.43 108.64 3.79 9.20e-01 1.18e+00 1.70e+01 angle pdb=" C ILE E 80 " pdb=" N PRO E 81 " pdb=" CA PRO E 81 " ideal model delta sigma weight residual 119.84 124.98 -5.14 1.25e+00 6.40e-01 1.69e+01 ... (remaining 20471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 7830 35.84 - 71.69: 274 71.69 - 107.53: 26 107.53 - 143.38: 5 143.38 - 179.22: 3 Dihedral angle restraints: 8138 sinusoidal: 4917 harmonic: 3221 Sorted by residual: dihedral pdb=" O4' U B 43 " pdb=" C1' U B 43 " pdb=" N1 U B 43 " pdb=" C2 U B 43 " ideal model delta sinusoidal sigma weight residual 232.00 52.78 179.22 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 133 " pdb=" C1' U B 133 " pdb=" N1 U B 133 " pdb=" C2 U B 133 " ideal model delta sinusoidal sigma weight residual -128.00 48.72 -176.72 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 291 " pdb=" C1' U B 291 " pdb=" N1 U B 291 " pdb=" C2 U B 291 " ideal model delta sinusoidal sigma weight residual -128.00 40.43 -168.43 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 8135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2400 0.113 - 0.227: 87 0.227 - 0.340: 8 0.340 - 0.454: 0 0.454 - 0.567: 1 Chirality restraints: 2496 Sorted by residual: chirality pdb=" P G B 251 " pdb=" OP1 G B 251 " pdb=" OP2 G B 251 " pdb=" O5' G B 251 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.05e+00 chirality pdb=" CA MET F 63 " pdb=" N MET F 63 " pdb=" C MET F 63 " pdb=" CB MET F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" P G B 319 " pdb=" OP1 G B 319 " pdb=" OP2 G B 319 " pdb=" O5' G B 319 " both_signs ideal model delta sigma weight residual True 2.41 -2.65 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2493 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 26 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C PHE E 26 " -0.052 2.00e-02 2.50e+03 pdb=" O PHE E 26 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO E 27 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 312 " -0.000 2.00e-02 2.50e+03 1.70e-02 6.49e+00 pdb=" N1 U B 312 " 0.015 2.00e-02 2.50e+03 pdb=" C2 U B 312 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U B 312 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U B 312 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 312 " -0.016 2.00e-02 2.50e+03 pdb=" O4 U B 312 " 0.000 2.00e-02 2.50e+03 pdb=" C5 U B 312 " 0.032 2.00e-02 2.50e+03 pdb=" C6 U B 312 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 43 " 0.023 2.00e-02 2.50e+03 1.70e-02 5.76e+00 pdb=" CG TYR F 43 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR F 43 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR F 43 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR F 43 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR F 43 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR F 43 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR F 43 " -0.002 2.00e-02 2.50e+03 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1519 2.75 - 3.28: 12437 3.28 - 3.82: 23235 3.82 - 4.36: 26628 4.36 - 4.90: 41800 Nonbonded interactions: 105619 Sorted by model distance: nonbonded pdb=" O LEU A1079 " pdb=" OG1 THR A1083 " model vdw 2.206 3.040 nonbonded pdb=" NE ARG E 78 " pdb=" O6 G B 315 " model vdw 2.221 3.120 nonbonded pdb=" O2' G B 71 " pdb=" OP1 C B 72 " model vdw 2.241 3.040 nonbonded pdb=" O TYR F 38 " pdb=" N VAL F 40 " model vdw 2.245 3.120 nonbonded pdb=" OG SER A 619 " pdb=" O ASN A 635 " model vdw 2.261 3.040 ... (remaining 105614 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.240 Find NCS groups from input model: 0.050 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.005 0.049 14328 Z= 0.328 Angle : 0.748 7.614 20476 Z= 0.471 Chirality : 0.049 0.567 2496 Planarity : 0.004 0.041 1776 Dihedral : 16.375 179.219 6052 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.33 % Rotamer: Outliers : 0.10 % Allowed : 1.26 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.26), residues: 1092 helix: 0.47 (0.23), residues: 546 sheet: -0.29 (0.51), residues: 93 loop : -1.38 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 470 TYR 0.024 0.002 TYR F 43 PHE 0.030 0.002 PHE F 66 TRP 0.015 0.001 TRP A 581 HIS 0.012 0.002 HIS F 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.33 (14328) covalent geometry : angle 0.74758 / 0.47 (20476) hydrogen bonds : bond 0.15745 / 9.62 ( 626) hydrogen bonds : angle 6.10120 / 4.27 ( 1674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.304 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: F 63 MET cc_start: 0.9253 (ptt) cc_final: 0.9052 (mmt) REVERT: E 37 LYS cc_start: 0.5136 (tptp) cc_final: 0.4891 (mptt) REVERT: E 62 GLU cc_start: 0.9252 (tp30) cc_final: 0.8818 (mm-30) REVERT: E 80 ILE cc_start: 0.6512 (tt) cc_final: 0.6153 (tp) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.1170 time to fit residues: 23.1959 Evaluate side-chains 85 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 GLN A 608 GLN A 827 GLN A1023 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.101151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065213 restraints weight = 47653.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067031 restraints weight = 23566.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.068077 restraints weight = 16531.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.068650 restraints weight = 13893.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.068871 restraints weight = 12802.979| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14328 Z= 0.154 Angle : 0.624 8.400 20476 Z= 0.312 Chirality : 0.036 0.182 2496 Planarity : 0.005 0.049 1776 Dihedral : 16.233 178.946 3911 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.15 % Allowed : 7.45 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1092 helix: 0.93 (0.22), residues: 564 sheet: -0.07 (0.51), residues: 93 loop : -1.21 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 901 TYR 0.019 0.001 TYR F 43 PHE 0.015 0.002 PHE F 66 TRP 0.010 0.001 TRP A 547 HIS 0.012 0.001 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (14328) covalent geometry : angle 0.62440 / 0.31 (20476) hydrogen bonds : bond 0.05595 / 3.86 ( 626) hydrogen bonds : angle 4.43099 / 3.12 ( 1674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 ARG cc_start: 0.7497 (mtm110) cc_final: 0.7135 (ptt-90) REVERT: E 62 GLU cc_start: 0.9079 (tp30) cc_final: 0.8771 (mm-30) REVERT: E 69 ASN cc_start: 0.9033 (m110) cc_final: 0.7990 (m110) REVERT: E 76 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8010 (mmmt) REVERT: A 512 MET cc_start: 0.8939 (mtp) cc_final: 0.8715 (mtp) REVERT: A 813 MET cc_start: 0.8447 (tmm) cc_final: 0.8093 (tmm) outliers start: 11 outliers final: 4 residues processed: 100 average time/residue: 0.1101 time to fit residues: 15.8314 Evaluate side-chains 89 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 0.0370 overall best weight: 2.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.099297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.062998 restraints weight = 48464.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.064793 restraints weight = 23939.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065826 restraints weight = 16856.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.066362 restraints weight = 14244.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066569 restraints weight = 13177.997| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14328 Z= 0.199 Angle : 0.613 8.919 20476 Z= 0.306 Chirality : 0.036 0.198 2496 Planarity : 0.005 0.084 1776 Dihedral : 16.147 176.541 3911 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.47 % Allowed : 10.39 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 1092 helix: 1.24 (0.22), residues: 568 sheet: -0.15 (0.51), residues: 93 loop : -1.12 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG E 72 TYR 0.035 0.002 TYR A 18 PHE 0.024 0.002 PHE F 66 TRP 0.011 0.001 TRP A 581 HIS 0.006 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (14328) covalent geometry : angle 0.61325 / 0.31 (20476) hydrogen bonds : bond 0.04993 / 3.45 ( 626) hydrogen bonds : angle 4.22875 / 3.00 ( 1674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 MET cc_start: 0.8992 (tmm) cc_final: 0.8008 (tmm) REVERT: E 18 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7408 (ptt-90) REVERT: E 62 GLU cc_start: 0.9152 (tp30) cc_final: 0.8838 (mm-30) REVERT: E 76 LYS cc_start: 0.8610 (mmtt) cc_final: 0.7860 (mmmt) REVERT: A 78 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8411 (tmtt) REVERT: A 512 MET cc_start: 0.9113 (mtp) cc_final: 0.8886 (mtp) REVERT: A 813 MET cc_start: 0.8699 (tmm) cc_final: 0.8130 (tmm) outliers start: 14 outliers final: 11 residues processed: 87 average time/residue: 0.1029 time to fit residues: 13.3049 Evaluate side-chains 86 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 TYR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1036 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 59 optimal weight: 40.0000 chunk 17 optimal weight: 30.0000 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 105 optimal weight: 0.0970 chunk 83 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 HIS A 687 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.099519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063186 restraints weight = 48377.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065005 restraints weight = 23767.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.066054 restraints weight = 16685.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066492 restraints weight = 14097.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.066835 restraints weight = 13139.164| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14328 Z= 0.154 Angle : 0.572 10.005 20476 Z= 0.286 Chirality : 0.034 0.179 2496 Planarity : 0.004 0.038 1776 Dihedral : 16.073 175.734 3911 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.68 % Allowed : 12.28 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 1092 helix: 1.36 (0.22), residues: 569 sheet: 0.05 (0.54), residues: 86 loop : -1.04 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 48 TYR 0.013 0.001 TYR F 38 PHE 0.015 0.002 PHE F 66 TRP 0.010 0.001 TRP A 581 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (14328) covalent geometry : angle 0.57203 / 0.29 (20476) hydrogen bonds : bond 0.04549 / 3.19 ( 626) hydrogen bonds : angle 4.07875 / 2.88 ( 1674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 38 TYR cc_start: 0.8468 (m-10) cc_final: 0.8232 (m-10) REVERT: E 62 GLU cc_start: 0.9133 (tp30) cc_final: 0.8811 (mm-30) REVERT: E 72 ARG cc_start: 0.8262 (ppt170) cc_final: 0.7725 (ppt170) REVERT: E 76 LYS cc_start: 0.8538 (mmtt) cc_final: 0.7944 (mmmt) REVERT: A 125 ASN cc_start: 0.7689 (t0) cc_final: 0.7449 (t0) REVERT: A 512 MET cc_start: 0.9100 (mtp) cc_final: 0.8884 (mtp) REVERT: A 813 MET cc_start: 0.8740 (tmm) cc_final: 0.8120 (tmm) outliers start: 16 outliers final: 8 residues processed: 83 average time/residue: 0.0853 time to fit residues: 11.0308 Evaluate side-chains 81 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 TYR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1036 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 69 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 17 optimal weight: 30.0000 chunk 78 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 17 HIS A 340 GLN A 762 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.097009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061200 restraints weight = 49518.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.062959 restraints weight = 24263.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063952 restraints weight = 17021.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.064478 restraints weight = 14400.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064657 restraints weight = 13322.761| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 14328 Z= 0.248 Angle : 0.648 10.128 20476 Z= 0.324 Chirality : 0.037 0.170 2496 Planarity : 0.005 0.033 1776 Dihedral : 16.163 175.899 3911 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.52 % Allowed : 14.17 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1092 helix: 1.18 (0.21), residues: 571 sheet: -0.19 (0.53), residues: 87 loop : -1.14 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 471 TYR 0.018 0.002 TYR F 43 PHE 0.028 0.002 PHE A 47 TRP 0.018 0.002 TRP A 60 HIS 0.007 0.001 HIS A1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.25 (14328) covalent geometry : angle 0.64811 / 0.32 (20476) hydrogen bonds : bond 0.05159 / 3.60 ( 626) hydrogen bonds : angle 4.17221 / 2.98 ( 1674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 117 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7427 (pttm) REVERT: E 18 ARG cc_start: 0.7769 (mtm110) cc_final: 0.7454 (ptt-90) REVERT: E 62 GLU cc_start: 0.9179 (tp30) cc_final: 0.8843 (mm-30) REVERT: E 74 ASN cc_start: 0.7629 (p0) cc_final: 0.7398 (p0) REVERT: E 76 LYS cc_start: 0.8637 (mmtt) cc_final: 0.7988 (mmmt) REVERT: A 512 MET cc_start: 0.9123 (mtp) cc_final: 0.8864 (mtp) outliers start: 24 outliers final: 15 residues processed: 91 average time/residue: 0.0914 time to fit residues: 12.8214 Evaluate side-chains 90 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 TYR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1090 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 30 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 0.0020 chunk 19 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 overall best weight: 3.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 64 ASN ** 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 = 0.3828 r_free = 0.3828 target = 0.097114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.061255 restraints weight = 49645.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.063017 restraints weight = 25105.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063997 restraints weight = 17927.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.064414 restraints weight = 15267.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.064754 restraints weight = 14282.497| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14328 Z= 0.225 Angle : 0.611 10.514 20476 Z= 0.308 Chirality : 0.036 0.176 2496 Planarity : 0.004 0.032 1776 Dihedral : 16.185 174.957 3911 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.20 % Allowed : 16.16 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1092 helix: 1.26 (0.21), residues: 569 sheet: -0.24 (0.52), residues: 87 loop : -1.15 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 87 TYR 0.024 0.002 TYR A 18 PHE 0.016 0.002 PHE A 331 TRP 0.013 0.001 TRP A 60 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.23 (14328) covalent geometry : angle 0.61065 / 0.31 (20476) hydrogen bonds : bond 0.04861 / 3.41 ( 626) hydrogen bonds : angle 4.12327 / 2.93 ( 1674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 117 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7524 (pttm) REVERT: E 62 GLU cc_start: 0.9237 (tp30) cc_final: 0.8843 (mm-30) REVERT: E 76 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8063 (mmmt) REVERT: A 512 MET cc_start: 0.9101 (mtp) cc_final: 0.8835 (mtp) outliers start: 21 outliers final: 13 residues processed: 86 average time/residue: 0.0957 time to fit residues: 12.7149 Evaluate side-chains 82 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 TYR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 125 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.098126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.062433 restraints weight = 49346.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.064212 restraints weight = 24893.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065212 restraints weight = 17717.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065741 restraints weight = 15096.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.065944 restraints weight = 14020.640| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14328 Z= 0.141 Angle : 0.563 11.160 20476 Z= 0.282 Chirality : 0.034 0.181 2496 Planarity : 0.004 0.032 1776 Dihedral : 16.110 174.352 3911 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.89 % Allowed : 16.89 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 1092 helix: 1.44 (0.22), residues: 573 sheet: -0.06 (0.53), residues: 87 loop : -1.02 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 48 TYR 0.013 0.001 TYR F 43 PHE 0.018 0.002 PHE A 47 TRP 0.014 0.001 TRP A 60 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (14328) covalent geometry : angle 0.56260 / 0.28 (20476) hydrogen bonds : bond 0.04380 / 3.07 ( 626) hydrogen bonds : angle 3.94129 / 2.80 ( 1674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 117 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7559 (pttm) REVERT: E 18 ARG cc_start: 0.7542 (mtm110) cc_final: 0.7264 (ptt-90) REVERT: E 62 GLU cc_start: 0.9220 (tp30) cc_final: 0.8835 (mm-30) REVERT: E 72 ARG cc_start: 0.8301 (ppt170) cc_final: 0.7781 (ppt170) REVERT: E 76 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8105 (mmmt) REVERT: A 512 MET cc_start: 0.9045 (mtp) cc_final: 0.8810 (mtp) outliers start: 18 outliers final: 15 residues processed: 88 average time/residue: 0.1015 time to fit residues: 13.5043 Evaluate side-chains 90 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 TYR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 827 GLN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 103 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.096047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.060738 restraints weight = 49430.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.062469 restraints weight = 24572.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063437 restraints weight = 17338.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063951 restraints weight = 14689.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064181 restraints weight = 13584.831| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14328 Z= 0.285 Angle : 0.664 10.139 20476 Z= 0.331 Chirality : 0.038 0.193 2496 Planarity : 0.005 0.047 1776 Dihedral : 16.193 174.980 3911 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.20 % Allowed : 17.52 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.26), residues: 1092 helix: 1.23 (0.21), residues: 574 sheet: -0.37 (0.52), residues: 87 loop : -1.11 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 672 TYR 0.016 0.002 TYR F 43 PHE 0.017 0.002 PHE A 331 TRP 0.010 0.002 TRP A 581 HIS 0.005 0.001 HIS A1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.29 (14328) covalent geometry : angle 0.66364 / 0.33 (20476) hydrogen bonds : bond 0.05105 / 3.58 ( 626) hydrogen bonds : angle 4.19714 / 3.00 ( 1674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 117 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7505 (pttm) REVERT: E 62 GLU cc_start: 0.9214 (tp30) cc_final: 0.8827 (mm-30) REVERT: E 76 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8113 (mmmt) REVERT: A 512 MET cc_start: 0.9128 (mtp) cc_final: 0.8892 (mtp) REVERT: A 813 MET cc_start: 0.8965 (tpt) cc_final: 0.8546 (tmm) outliers start: 21 outliers final: 16 residues processed: 85 average time/residue: 0.0811 time to fit residues: 10.7481 Evaluate side-chains 86 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 TYR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 39 optimal weight: 0.0070 chunk 17 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 41 optimal weight: 0.0370 chunk 47 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 overall best weight: 2.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.097236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062180 restraints weight = 49460.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063959 restraints weight = 23955.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.065001 restraints weight = 16655.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065548 restraints weight = 14000.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.065696 restraints weight = 12891.552| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14328 Z= 0.166 Angle : 0.586 11.263 20476 Z= 0.293 Chirality : 0.035 0.184 2496 Planarity : 0.004 0.032 1776 Dihedral : 16.148 173.683 3911 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.78 % Allowed : 17.84 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 1092 helix: 1.31 (0.22), residues: 575 sheet: -0.18 (0.53), residues: 87 loop : -1.05 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG F 87 TYR 0.016 0.001 TYR F 43 PHE 0.014 0.002 PHE A 331 TRP 0.011 0.001 TRP A 547 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (14328) covalent geometry : angle 0.58560 / 0.29 (20476) hydrogen bonds : bond 0.04554 / 3.19 ( 626) hydrogen bonds : angle 4.00971 / 2.86 ( 1674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 117 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7511 (pttm) REVERT: E 62 GLU cc_start: 0.9208 (tp30) cc_final: 0.8833 (mm-30) REVERT: E 72 ARG cc_start: 0.8348 (ppt170) cc_final: 0.7791 (ppt170) REVERT: E 76 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8114 (mmmt) REVERT: A 512 MET cc_start: 0.9073 (mtp) cc_final: 0.8844 (mtp) REVERT: A 813 MET cc_start: 0.8951 (tpt) cc_final: 0.8551 (tmm) outliers start: 17 outliers final: 15 residues processed: 82 average time/residue: 0.0975 time to fit residues: 12.1806 Evaluate side-chains 87 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 TYR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 123 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.098359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.063413 restraints weight = 48999.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065255 restraints weight = 23514.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066307 restraints weight = 16223.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.066847 restraints weight = 13597.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.067109 restraints weight = 12545.136| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14328 Z= 0.116 Angle : 0.546 11.584 20476 Z= 0.274 Chirality : 0.033 0.186 2496 Planarity : 0.004 0.032 1776 Dihedral : 16.008 173.579 3911 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.57 % Allowed : 18.05 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.26), residues: 1092 helix: 1.54 (0.22), residues: 572 sheet: -0.03 (0.54), residues: 87 loop : -0.99 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 78 TYR 0.011 0.001 TYR F 43 PHE 0.011 0.001 PHE A 331 TRP 0.032 0.002 TRP A 60 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (14328) covalent geometry : angle 0.54630 / 0.27 (20476) hydrogen bonds : bond 0.04062 / 2.84 ( 626) hydrogen bonds : angle 3.84429 / 2.73 ( 1674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 TYR cc_start: 0.7653 (t80) cc_final: 0.7124 (t80) REVERT: E 62 GLU cc_start: 0.9192 (tp30) cc_final: 0.8805 (mm-30) REVERT: E 72 ARG cc_start: 0.8311 (ppt170) cc_final: 0.7756 (ppt170) REVERT: E 76 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8137 (mmmt) REVERT: A 813 MET cc_start: 0.8908 (tpt) cc_final: 0.8573 (tmm) REVERT: A 1038 ASP cc_start: 0.8700 (m-30) cc_final: 0.8489 (m-30) outliers start: 15 outliers final: 14 residues processed: 84 average time/residue: 0.0916 time to fit residues: 11.6209 Evaluate side-chains 87 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 TYR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 63 optimal weight: 0.0020 chunk 53 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 61 optimal weight: 0.1980 overall best weight: 1.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.097934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062786 restraints weight = 49232.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064617 restraints weight = 23769.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.065662 restraints weight = 16480.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066205 restraints weight = 13845.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.066417 restraints weight = 12762.420| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14328 Z= 0.142 Angle : 0.557 10.987 20476 Z= 0.277 Chirality : 0.034 0.187 2496 Planarity : 0.004 0.035 1776 Dihedral : 15.971 173.904 3911 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.26 % Allowed : 18.47 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 1092 helix: 1.58 (0.22), residues: 571 sheet: 0.02 (0.55), residues: 87 loop : -0.97 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 72 TYR 0.016 0.001 TYR F 38 PHE 0.016 0.001 PHE E 26 TRP 0.020 0.001 TRP A 60 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14328) covalent geometry : angle 0.55672 / 0.28 (20476) hydrogen bonds : bond 0.04135 / 2.89 ( 626) hydrogen bonds : angle 3.85788 / 2.74 ( 1674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.78 seconds wall clock time: 37 minutes 16.08 seconds (2236.08 seconds total)