Starting phenix.real_space_refine on Sun Oct 25 10:18:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ne9_49302/10_2026/9ne9_49302.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ne9_49302/10_2026/9ne9_49302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ne9_49302/10_2026/9ne9_49302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ne9_49302/10_2026/9ne9_49302.map" model { file = "/net/cci-nas-00/data/ceres_data/9ne9_49302/10_2026/9ne9_49302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ne9_49302/10_2026/9ne9_49302.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 65 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 10392 2.51 5 N 2824 2.21 5 O 3345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16735 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9367 Classifications: {'peptide': 1152} Link IDs: {'PTRANS': 58, 'TRANS': 1093} Chain breaks: 1 Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "D" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "P" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 659 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 675 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Unusual residues: {' MG': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4994 SG CYS A 663 27.903 29.883 47.102 1.00109.15 S ATOM 4928 SG CYS A 654 23.519 34.446 46.644 1.00133.43 S ATOM 5718 SG CYS A 747 30.235 35.257 48.756 1.00 83.15 S ATOM 4912 SG CYS A 651 27.287 33.098 52.090 1.00123.77 S Time building chain proxies: 3.84, per 1000 atoms: 0.23 Number of scatterers: 16735 At special positions: 0 Unit cell: (103.5, 103.5, 157.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 103 16.00 P 65 15.00 Mg 2 11.99 O 3345 8.00 N 2824 7.00 C 10392 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: 1.52 Conformation dependent library (CDL) restraints added in 616.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1203 " pdb="FE3 SF4 A1203 " - pdb=" SG CYS A 747 " pdb="FE1 SF4 A1203 " - pdb=" SG CYS A 663 " pdb="FE2 SF4 A1203 " - pdb=" SG CYS A 654 " pdb="FE4 SF4 A1203 " - pdb=" SG CYS A 651 " Number of angles added : 12 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3684 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 17 sheets defined 32.8% alpha, 19.8% beta 31 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 112 through 124 removed outlier: 4.176A pdb=" N VAL A 116 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.882A pdb=" N VAL A 146 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 193 Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 367 through 379 removed outlier: 3.794A pdb=" N PHE A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 443 through 451 removed outlier: 3.817A pdb=" N THR A 449 " --> pdb=" O CYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 472 removed outlier: 4.358A pdb=" N LEU A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 496 through 512 Processing helix chain 'A' and resid 563 through 585 removed outlier: 3.842A pdb=" N PHE A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLU A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LYS A 576 " --> pdb=" O GLN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 612 removed outlier: 4.001A pdb=" N VAL A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP A 612 " --> pdb=" O ALA A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 removed outlier: 4.487A pdb=" N ASN A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 654 Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 711 through 727 removed outlier: 3.656A pdb=" N GLN A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 786 removed outlier: 3.570A pdb=" N THR A 757 " --> pdb=" O PHE A 753 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU A 784 " --> pdb=" O SER A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 820 removed outlier: 4.787A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 851 Processing helix chain 'A' and resid 892 through 905 removed outlier: 3.670A pdb=" N PHE A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 991 removed outlier: 4.362A pdb=" N ILE A 984 " --> pdb=" O GLN A 980 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1019 Processing helix chain 'A' and resid 1026 through 1034 removed outlier: 4.224A pdb=" N GLU A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A1034 " --> pdb=" O PHE A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1064 removed outlier: 3.648A pdb=" N LEU A1064 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1071 removed outlier: 3.656A pdb=" N VAL A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A1071 " --> pdb=" O GLN A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1091 Processing helix chain 'A' and resid 1097 through 1101 removed outlier: 3.581A pdb=" N GLN A1100 " --> pdb=" O ALA A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1114 Processing helix chain 'A' and resid 1129 through 1145 Processing helix chain 'A' and resid 1145 through 1151 Processing helix chain 'A' and resid 1164 through 1175 Processing helix chain 'B' and resid 9 through 20 removed outlier: 4.210A pdb=" N LEU B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 155 removed outlier: 4.156A pdb=" N HIS B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 154 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'C' and resid 9 through 19 removed outlier: 3.767A pdb=" N LYS C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.993A pdb=" N LYS C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 149 Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.614A pdb=" N ASN C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 209 through 214' Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.621A pdb=" N LEU C 221 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 17 removed outlier: 3.670A pdb=" N LYS D 13 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 78 removed outlier: 3.602A pdb=" N LYS D 77 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 209 through 216 removed outlier: 4.190A pdb=" N PHE D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 99 removed outlier: 7.541A pdb=" N ALA A 81 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP A 83 " --> pdb=" O MET A 66 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N MET A 66 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR A 85 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 132 removed outlier: 3.640A pdb=" N TYR A 105 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 337 removed outlier: 6.716A pdb=" N GLY A 304 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE A 335 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU A 306 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLU A 337 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR A 308 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N MET A 294 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET A 295 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET A 359 " --> pdb=" O MET A 405 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 534 through 538 removed outlier: 3.786A pdb=" N ARG A 665 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR A 745 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 546 Processing sheet with id=AA6, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 561 Processing sheet with id=AA8, first strand: chain 'A' and resid 620 through 625 Processing sheet with id=AA9, first strand: chain 'A' and resid 875 through 879 Processing sheet with id=AB1, first strand: chain 'A' and resid 1035 through 1037 Processing sheet with id=AB2, first strand: chain 'A' and resid 1179 through 1180 removed outlier: 3.764A pdb=" N LYS A1179 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 255 " --> pdb=" O LYS A1179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 60 through 61 removed outlier: 4.200A pdb=" N VAL B 111 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS C 181 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 113 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN C 179 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 115 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN C 177 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.650A pdb=" N LEU B 247 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 203 through 208 removed outlier: 3.592A pdb=" N VAL D 111 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU D 3 " --> pdb=" O ARG D 61 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG D 61 " --> pdb=" O GLU D 3 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.813A pdb=" N ASP C 29 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS C 246 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 104 removed outlier: 3.554A pdb=" N VAL C 111 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY D 178 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 167 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 157 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 66 through 68 removed outlier: 4.818A pdb=" N LYS D 240 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR D 224 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR D 196 " --> pdb=" O LYS D 138 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 6775 1.39 - 1.61: 10246 1.61 - 1.84: 161 1.84 - 2.06: 0 2.06 - 2.28: 13 Bond restraints: 17195 Sorted by residual: bond pdb=" C4' PST P 35 " pdb=" O4' PST P 35 " ideal model delta sigma weight residual 1.420 1.663 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C4' PST P 35 " pdb=" C3' PST P 35 " ideal model delta sigma weight residual 1.525 1.340 0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" P PST P 35 " pdb=" SP PST P 35 " ideal model delta sigma weight residual 1.925 2.103 -0.178 2.00e-02 2.50e+03 7.95e+01 bond pdb=" O4' PST P 35 " pdb=" C1' PST P 35 " ideal model delta sigma weight residual 1.400 1.303 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C4 PST P 35 " pdb=" C5 PST P 35 " ideal model delta sigma weight residual 1.448 1.353 0.095 2.00e-02 2.50e+03 2.28e+01 ... (remaining 17190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 23134 3.13 - 6.25: 314 6.25 - 9.38: 61 9.38 - 12.50: 6 12.50 - 15.63: 1 Bond angle restraints: 23516 Sorted by residual: angle pdb=" C3' DA P 34 " pdb=" O3' DA P 34 " pdb=" P PST P 35 " ideal model delta sigma weight residual 119.70 135.33 -15.63 1.20e+00 6.94e-01 1.70e+02 angle pdb=" C ASP A 787 " pdb=" N ALA A 788 " pdb=" CA ALA A 788 " ideal model delta sigma weight residual 120.82 127.68 -6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" CA ASP A 235 " pdb=" CB ASP A 235 " pdb=" CG ASP A 235 " ideal model delta sigma weight residual 112.60 117.14 -4.54 1.00e+00 1.00e+00 2.06e+01 angle pdb=" N ALA A 788 " pdb=" CA ALA A 788 " pdb=" C ALA A 788 " ideal model delta sigma weight residual 111.37 118.53 -7.16 1.65e+00 3.67e-01 1.88e+01 angle pdb=" N3 DT P 24 " pdb=" C4 DT P 24 " pdb=" O4 DT P 24 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 23511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 8861 17.55 - 35.11: 1038 35.11 - 52.66: 361 52.66 - 70.22: 81 70.22 - 87.77: 21 Dihedral angle restraints: 10362 sinusoidal: 4678 harmonic: 5684 Sorted by residual: dihedral pdb=" CA GLU C 198 " pdb=" C GLU C 198 " pdb=" N MET C 199 " pdb=" CA MET C 199 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA ILE A 276 " pdb=" C ILE A 276 " pdb=" N GLU A 277 " pdb=" CA GLU A 277 " ideal model delta harmonic sigma weight residual 180.00 152.66 27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ASP A 626 " pdb=" C ASP A 626 " pdb=" N VAL A 627 " pdb=" CA VAL A 627 " ideal model delta harmonic sigma weight residual 180.00 153.04 26.96 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 10359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2292 0.083 - 0.167: 308 0.167 - 0.250: 20 0.250 - 0.334: 2 0.334 - 0.417: 1 Chirality restraints: 2623 Sorted by residual: chirality pdb=" CB ILE A 300 " pdb=" CA ILE A 300 " pdb=" CG1 ILE A 300 " pdb=" CG2 ILE A 300 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CB VAL A 791 " pdb=" CA VAL A 791 " pdb=" CG1 VAL A 791 " pdb=" CG2 VAL A 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB ILE A 635 " pdb=" CA ILE A 635 " pdb=" CG1 ILE A 635 " pdb=" CG2 ILE A 635 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2620 not shown) Planarity restraints: 2804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 552 " 0.022 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE A 552 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 552 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 552 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 552 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 552 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 552 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1083 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO A1084 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A1084 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1084 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 233 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO B 234 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " -0.033 5.00e-02 4.00e+02 ... (remaining 2801 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 6803 2.95 - 3.44: 17082 3.44 - 3.93: 28117 3.93 - 4.41: 30721 4.41 - 4.90: 48920 Nonbonded interactions: 131643 Sorted by model distance: nonbonded pdb=" OD2 ASP A 275 " pdb="MG MG A1202 " model vdw 2.464 2.170 nonbonded pdb=" O SER D 134 " pdb=" OG SER D 228 " model vdw 2.474 3.040 nonbonded pdb=" N ALA A 129 " pdb=" O SER A 156 " model vdw 2.540 3.120 nonbonded pdb=" O PRO D 129 " pdb=" OH TYR D 133 " model vdw 2.548 3.040 nonbonded pdb=" CA GLY C 166 " pdb=" O LEU C 182 " model vdw 2.553 2.752 ... (remaining 131638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.720 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.243 17199 Z= 0.370 Angle : 1.061 35.469 23528 Z= 0.590 Chirality : 0.056 0.417 2623 Planarity : 0.006 0.065 2804 Dihedral : 17.506 87.769 6678 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.29 % Allowed : 0.59 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.18), residues: 1925 helix: -1.26 (0.20), residues: 587 sheet: -0.85 (0.23), residues: 466 loop : -1.71 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 976 TYR 0.026 0.002 TYR A 244 PHE 0.057 0.003 PHE A 552 TRP 0.036 0.002 TRP A 826 HIS 0.014 0.002 HIS A 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.37 (17195) covalent geometry : angle 1.00045 / 0.59 (23516) hydrogen bonds : bond 0.11769 / 7.83 ( 777) hydrogen bonds : angle 6.43248 / 4.49 ( 2113) metal coordination : bond 0.00319 / 0.16 ( 4) metal coordination : angle 15.73923 / 8.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 319 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.7397 (m-80) cc_final: 0.7020 (m-10) REVERT: A 178 ARG cc_start: 0.3632 (OUTLIER) cc_final: 0.2272 (ttp-170) REVERT: A 219 VAL cc_start: 0.6657 (t) cc_final: 0.6118 (t) REVERT: A 224 TYR cc_start: 0.7192 (p90) cc_final: 0.6817 (p90) REVERT: A 362 TYR cc_start: 0.7578 (t80) cc_final: 0.7350 (t80) REVERT: A 645 MET cc_start: 0.7467 (ptp) cc_final: 0.7244 (ptp) REVERT: A 820 MET cc_start: 0.6777 (mmp) cc_final: 0.5784 (tpp) REVERT: A 905 PHE cc_start: 0.4960 (m-80) cc_final: 0.4698 (m-10) REVERT: A 983 LYS cc_start: 0.7547 (mmtp) cc_final: 0.7299 (mmtp) REVERT: A 1018 TYR cc_start: 0.6073 (t80) cc_final: 0.5815 (t80) REVERT: A 1197 MET cc_start: -0.0299 (mmt) cc_final: -0.3339 (ttp) REVERT: B 64 ARG cc_start: 0.7892 (pmt-80) cc_final: 0.7635 (pmt-80) REVERT: D 115 GLU cc_start: 0.7351 (pp20) cc_final: 0.7009 (mp0) outliers start: 5 outliers final: 0 residues processed: 322 average time/residue: 0.1457 time to fit residues: 67.8627 Evaluate side-chains 217 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 77, 122, 91] chunk 98 optimal weight: 0.0980 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.195688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.164141 restraints weight = 29718.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.163591 restraints weight = 23669.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.164064 restraints weight = 21011.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.164612 restraints weight = 19472.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.164779 restraints weight = 17818.633| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17199 Z= 0.191 Angle : 0.805 43.189 23528 Z= 0.379 Chirality : 0.045 0.187 2623 Planarity : 0.005 0.055 2804 Dihedral : 17.288 77.559 2839 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.17 % Allowed : 8.50 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.18), residues: 1925 helix: -0.52 (0.21), residues: 596 sheet: -0.70 (0.24), residues: 466 loop : -1.70 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1059 TYR 0.017 0.002 TYR A 892 PHE 0.032 0.002 PHE A1109 TRP 0.019 0.002 TRP A 826 HIS 0.009 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (17195) covalent geometry : angle 0.71273 / 0.38 (23516) hydrogen bonds : bond 0.04692 / 3.02 ( 777) hydrogen bonds : angle 5.54507 / 3.84 ( 2113) metal coordination : bond 0.00489 / 0.25 ( 4) metal coordination : angle 16.58561 / 9.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.7047 (tm-30) cc_final: 0.6751 (tm-30) REVERT: A 176 LYS cc_start: 0.8516 (tptp) cc_final: 0.8222 (tppt) REVERT: A 645 MET cc_start: 0.7519 (ptp) cc_final: 0.7292 (ptp) REVERT: A 831 MET cc_start: 0.6846 (tmm) cc_final: 0.6287 (tmm) REVERT: A 951 LYS cc_start: 0.7678 (ptpp) cc_final: 0.6885 (mmtt) REVERT: A 983 LYS cc_start: 0.7617 (mmtp) cc_final: 0.7349 (mmtm) REVERT: A 1197 MET cc_start: -0.0235 (mmt) cc_final: -0.3647 (ttp) REVERT: B 20 LYS cc_start: 0.7337 (ptpp) cc_final: 0.7048 (ttmt) REVERT: C 1 MET cc_start: 0.2800 (ttt) cc_final: 0.2518 (tpt) outliers start: 20 outliers final: 17 residues processed: 243 average time/residue: 0.1310 time to fit residues: 47.1144 Evaluate side-chains 220 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: [158, 194, 7, 39, 76, 198, 178, 14, 63, 132, 153] chunk 158 optimal weight: 9.9990 chunk 194 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 198 optimal weight: 40.0000 chunk 178 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 HIS ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.195615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.164486 restraints weight = 29929.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.163666 restraints weight = 22835.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.164232 restraints weight = 21022.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.164924 restraints weight = 19008.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.165150 restraints weight = 16941.605| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17199 Z= 0.157 Angle : 0.750 41.640 23528 Z= 0.348 Chirality : 0.044 0.166 2623 Planarity : 0.004 0.052 2804 Dihedral : 17.250 77.841 2835 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.70 % Allowed : 11.96 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.19), residues: 1925 helix: -0.24 (0.21), residues: 599 sheet: -0.73 (0.24), residues: 476 loop : -1.57 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 167 TYR 0.013 0.002 TYR D 250 PHE 0.036 0.002 PHE A 552 TRP 0.016 0.002 TRP A 826 HIS 0.006 0.001 HIS A 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (17195) covalent geometry : angle 0.65869 / 0.35 (23516) hydrogen bonds : bond 0.04269 / 2.78 ( 777) hydrogen bonds : angle 5.34366 / 3.71 ( 2113) metal coordination : bond 0.00426 / 0.22 ( 4) metal coordination : angle 15.88391 / 8.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.7010 (tm-30) cc_final: 0.6705 (tm-30) REVERT: A 128 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.7049 (pt) REVERT: A 176 LYS cc_start: 0.8463 (tptp) cc_final: 0.8189 (tppt) REVERT: A 178 ARG cc_start: 0.4201 (OUTLIER) cc_final: 0.1721 (tmm160) REVERT: A 831 MET cc_start: 0.6925 (tmm) cc_final: 0.6378 (tmm) REVERT: A 905 PHE cc_start: 0.4657 (m-80) cc_final: 0.4357 (m-10) REVERT: A 983 LYS cc_start: 0.7668 (mmtp) cc_final: 0.7403 (mmtm) REVERT: A 1197 MET cc_start: -0.0215 (mmt) cc_final: -0.3751 (ttp) REVERT: C 1 MET cc_start: 0.2696 (OUTLIER) cc_final: 0.2428 (tpt) REVERT: C 108 GLN cc_start: 0.7625 (mp-120) cc_final: 0.7373 (mp-120) outliers start: 29 outliers final: 18 residues processed: 230 average time/residue: 0.1299 time to fit residues: 44.6125 Evaluate side-chains 216 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 244 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: [127, 53, 135, 44, 191, 124, 18, 169, 123, 11, 80] chunk 127 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 169 optimal weight: 0.0470 chunk 123 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 HIS ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.196217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.165677 restraints weight = 29672.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.164989 restraints weight = 22969.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.165185 restraints weight = 20287.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.165681 restraints weight = 19469.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.165965 restraints weight = 17798.154| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17199 Z= 0.132 Angle : 0.710 38.089 23528 Z= 0.330 Chirality : 0.043 0.165 2623 Planarity : 0.004 0.054 2804 Dihedral : 17.245 78.061 2835 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.76 % Allowed : 14.02 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.19), residues: 1925 helix: -0.05 (0.21), residues: 600 sheet: -0.66 (0.24), residues: 484 loop : -1.44 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 167 TYR 0.015 0.001 TYR A 244 PHE 0.024 0.002 PHE A 753 TRP 0.017 0.001 TRP A 826 HIS 0.009 0.001 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (17195) covalent geometry : angle 0.62493 / 0.33 (23516) hydrogen bonds : bond 0.03955 / 2.57 ( 777) hydrogen bonds : angle 5.17530 / 3.59 ( 2113) metal coordination : bond 0.00427 / 0.22 ( 4) metal coordination : angle 14.91708 / 8.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LYS cc_start: 0.8488 (tptp) cc_final: 0.8180 (tppt) REVERT: A 178 ARG cc_start: 0.4210 (OUTLIER) cc_final: 0.1782 (tmm160) REVERT: A 505 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8656 (mm) REVERT: A 626 ASP cc_start: 0.5892 (p0) cc_final: 0.5106 (p0) REVERT: A 820 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.5650 (tpp) REVERT: A 831 MET cc_start: 0.6962 (tmm) cc_final: 0.6330 (tmm) REVERT: A 905 PHE cc_start: 0.4589 (m-80) cc_final: 0.4300 (m-10) REVERT: A 983 LYS cc_start: 0.7620 (mmtp) cc_final: 0.7341 (mmtm) REVERT: A 1197 MET cc_start: -0.0211 (mmt) cc_final: -0.3808 (ttp) REVERT: C 1 MET cc_start: 0.2551 (OUTLIER) cc_final: 0.2296 (tpt) REVERT: C 108 GLN cc_start: 0.7605 (mp-120) cc_final: 0.7365 (mp-120) REVERT: D 211 TYR cc_start: 0.8000 (m-80) cc_final: 0.7632 (m-80) outliers start: 30 outliers final: 18 residues processed: 221 average time/residue: 0.1272 time to fit residues: 42.0445 Evaluate side-chains 215 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 244 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: [54, 174, 85, 32, 152, 61, 120, 42, 175, 121, 179] chunk 54 optimal weight: 0.2980 chunk 174 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 chunk 61 optimal weight: 0.0010 chunk 120 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 175 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.193702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.160941 restraints weight = 27594.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.162461 restraints weight = 24549.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.163807 restraints weight = 18651.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.164284 restraints weight = 15038.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.164308 restraints weight = 14527.911| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17199 Z= 0.116 Angle : 0.684 34.559 23528 Z= 0.318 Chirality : 0.042 0.163 2623 Planarity : 0.004 0.050 2804 Dihedral : 17.233 78.337 2835 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.64 % Allowed : 14.60 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.19), residues: 1925 helix: 0.14 (0.21), residues: 601 sheet: -0.52 (0.24), residues: 469 loop : -1.36 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 167 TYR 0.015 0.001 TYR A 244 PHE 0.032 0.001 PHE A 552 TRP 0.014 0.001 TRP A 826 HIS 0.005 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (17195) covalent geometry : angle 0.60645 / 0.32 (23516) hydrogen bonds : bond 0.03744 / 2.44 ( 777) hydrogen bonds : angle 5.05394 / 3.51 ( 2113) metal coordination : bond 0.00343 / 0.18 ( 4) metal coordination : angle 14.00699 / 7.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LYS cc_start: 0.8517 (tptp) cc_final: 0.8135 (tppt) REVERT: A 178 ARG cc_start: 0.4165 (OUTLIER) cc_final: 0.1795 (tmm160) REVERT: A 626 ASP cc_start: 0.5807 (p0) cc_final: 0.5036 (p0) REVERT: A 820 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.5627 (tpp) REVERT: A 831 MET cc_start: 0.6949 (tmm) cc_final: 0.6181 (tmm) REVERT: A 905 PHE cc_start: 0.4605 (m-80) cc_final: 0.4358 (m-10) REVERT: A 983 LYS cc_start: 0.7629 (mmtp) cc_final: 0.7304 (mmtm) REVERT: A 1197 MET cc_start: -0.0214 (mmt) cc_final: -0.3855 (ttp) REVERT: C 1 MET cc_start: 0.2472 (OUTLIER) cc_final: 0.2246 (tpt) REVERT: D 211 TYR cc_start: 0.8070 (m-80) cc_final: 0.7692 (m-80) outliers start: 28 outliers final: 19 residues processed: 219 average time/residue: 0.1225 time to fit residues: 40.8330 Evaluate side-chains 212 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 244 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: [1, 155, 150, 57, 159, 13, 114, 63, 185, 174, 26] chunk 1 optimal weight: 7.9990 chunk 155 optimal weight: 0.4980 chunk 150 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN A 525 ASN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN C 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.184664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.150122 restraints weight = 27670.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.150937 restraints weight = 24095.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.152079 restraints weight = 19371.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.152675 restraints weight = 16031.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.152615 restraints weight = 15118.361| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 17199 Z= 0.302 Angle : 0.870 36.759 23528 Z= 0.419 Chirality : 0.049 0.180 2623 Planarity : 0.005 0.055 2804 Dihedral : 17.406 77.440 2835 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.87 % Allowed : 15.84 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.19), residues: 1925 helix: -0.37 (0.21), residues: 609 sheet: -0.75 (0.24), residues: 479 loop : -1.53 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 749 TYR 0.029 0.003 TYR A 892 PHE 0.028 0.003 PHE A 872 TRP 0.013 0.002 TRP D 28 HIS 0.009 0.002 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.30 (17195) covalent geometry : angle 0.80561 / 0.42 (23516) hydrogen bonds : bond 0.05169 / 3.40 ( 777) hydrogen bonds : angle 5.46996 / 3.82 ( 2113) metal coordination : bond 0.00742 / 0.38 ( 4) metal coordination : angle 14.55371 / 8.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ARG cc_start: 0.7726 (mtt90) cc_final: 0.5987 (mtt-85) REVERT: A 176 LYS cc_start: 0.8603 (tptp) cc_final: 0.8216 (tppt) REVERT: A 405 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.6004 (mtt) REVERT: A 715 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: A 831 MET cc_start: 0.7451 (tmm) cc_final: 0.6876 (tmm) REVERT: A 940 MET cc_start: 0.7634 (tpp) cc_final: 0.6793 (ttt) REVERT: A 947 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7142 (pp20) REVERT: A 1197 MET cc_start: -0.0305 (mmt) cc_final: -0.4055 (ttp) REVERT: B 147 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7157 (mm) REVERT: B 199 MET cc_start: 0.5326 (tpt) cc_final: 0.4775 (tpt) REVERT: C 1 MET cc_start: 0.3227 (OUTLIER) cc_final: 0.2864 (tpt) outliers start: 49 outliers final: 31 residues processed: 223 average time/residue: 0.1157 time to fit residues: 40.2380 Evaluate side-chains 216 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 715 GLN Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 244 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: [193, 93, 58, 125, 172, 22, 159, 42, 99, 112, 64] chunk 193 optimal weight: 50.0000 chunk 93 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.189810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.155809 restraints weight = 27303.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.156385 restraints weight = 23898.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.157821 restraints weight = 19497.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.157984 restraints weight = 16674.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.158084 restraints weight = 15345.001| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17199 Z= 0.137 Angle : 0.740 34.564 23528 Z= 0.345 Chirality : 0.044 0.165 2623 Planarity : 0.004 0.050 2804 Dihedral : 17.332 78.411 2835 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.23 % Allowed : 17.65 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.19), residues: 1925 helix: -0.10 (0.21), residues: 609 sheet: -0.65 (0.24), residues: 476 loop : -1.39 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 167 TYR 0.018 0.001 TYR A 244 PHE 0.030 0.002 PHE A 753 TRP 0.016 0.002 TRP A 671 HIS 0.007 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (17195) covalent geometry : angle 0.66608 / 0.34 (23516) hydrogen bonds : bond 0.04011 / 2.63 ( 777) hydrogen bonds : angle 5.17437 / 3.60 ( 2113) metal coordination : bond 0.00349 / 0.18 ( 4) metal coordination : angle 14.28410 / 8.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ARG cc_start: 0.7548 (mtt90) cc_final: 0.5661 (mtt-85) REVERT: A 176 LYS cc_start: 0.8549 (tptp) cc_final: 0.8208 (tppt) REVERT: A 230 ILE cc_start: 0.8167 (mm) cc_final: 0.7954 (mt) REVERT: A 405 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5772 (mtt) REVERT: A 571 LEU cc_start: 0.7249 (pp) cc_final: 0.7018 (pp) REVERT: A 626 ASP cc_start: 0.6214 (p0) cc_final: 0.4841 (p0) REVERT: A 831 MET cc_start: 0.7289 (tmm) cc_final: 0.6658 (tmm) REVERT: A 905 PHE cc_start: 0.4725 (m-80) cc_final: 0.4351 (m-10) REVERT: A 1197 MET cc_start: -0.0392 (mmt) cc_final: -0.4083 (ttp) REVERT: B 199 MET cc_start: 0.5456 (tpt) cc_final: 0.4871 (tpt) REVERT: C 1 MET cc_start: 0.2818 (OUTLIER) cc_final: 0.2516 (tpt) REVERT: D 211 TYR cc_start: 0.8061 (m-80) cc_final: 0.7711 (m-80) outliers start: 38 outliers final: 26 residues processed: 222 average time/residue: 0.1233 time to fit residues: 42.0095 Evaluate side-chains 216 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: [193, 139, 39, 57, 97, 156, 128, 15, 61, 37, 119] chunk 193 optimal weight: 50.0000 chunk 139 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 156 optimal weight: 0.5980 chunk 128 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 0.0270 chunk 119 optimal weight: 0.0170 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.191494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.156239 restraints weight = 27481.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.157668 restraints weight = 20100.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.157798 restraints weight = 16938.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.158276 restraints weight = 15698.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.158546 restraints weight = 14796.472| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17199 Z= 0.124 Angle : 0.715 31.181 23528 Z= 0.335 Chirality : 0.043 0.199 2623 Planarity : 0.004 0.047 2804 Dihedral : 17.260 78.913 2835 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.05 % Allowed : 17.54 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.19), residues: 1925 helix: 0.15 (0.22), residues: 603 sheet: -0.55 (0.24), residues: 485 loop : -1.31 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 167 TYR 0.015 0.001 TYR A 298 PHE 0.041 0.002 PHE A 552 TRP 0.015 0.001 TRP A 671 HIS 0.006 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (17195) covalent geometry : angle 0.64782 / 0.33 (23516) hydrogen bonds : bond 0.03849 / 2.52 ( 777) hydrogen bonds : angle 5.04680 / 3.51 ( 2113) metal coordination : bond 0.00324 / 0.17 ( 4) metal coordination : angle 13.40927 / 7.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ARG cc_start: 0.7552 (mtt90) cc_final: 0.5530 (mtt-85) REVERT: A 176 LYS cc_start: 0.8628 (tptp) cc_final: 0.8226 (tppt) REVERT: A 178 ARG cc_start: 0.4603 (OUTLIER) cc_final: 0.2499 (ttp-170) REVERT: A 405 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.5785 (mtt) REVERT: A 611 LYS cc_start: 0.6052 (mmtt) cc_final: 0.5837 (mmtt) REVERT: A 626 ASP cc_start: 0.6075 (p0) cc_final: 0.4661 (p0) REVERT: A 820 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.5731 (tpp) REVERT: A 831 MET cc_start: 0.7227 (tmm) cc_final: 0.6414 (tmm) REVERT: A 905 PHE cc_start: 0.4888 (m-80) cc_final: 0.4511 (m-10) REVERT: A 1197 MET cc_start: -0.0392 (mmt) cc_final: -0.4021 (ttp) REVERT: B 199 MET cc_start: 0.5531 (tpt) cc_final: 0.4944 (tpt) REVERT: C 1 MET cc_start: 0.2917 (OUTLIER) cc_final: 0.2517 (tpt) REVERT: C 8 GLN cc_start: 0.7521 (pp30) cc_final: 0.6441 (pm20) REVERT: D 211 TYR cc_start: 0.8084 (m-80) cc_final: 0.7732 (m-80) outliers start: 35 outliers final: 26 residues processed: 217 average time/residue: 0.1152 time to fit residues: 38.7830 Evaluate side-chains 213 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 151 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: [29, 102, 183, 137, 135, 60, 42, 129, 61, 112, 36] chunk 29 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 137 optimal weight: 0.3980 chunk 135 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4528 r_free = 0.4528 target = 0.191319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.157766 restraints weight = 27454.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.157456 restraints weight = 23028.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.158425 restraints weight = 17945.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.159244 restraints weight = 15814.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.159403 restraints weight = 14907.944| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17199 Z= 0.126 Angle : 0.711 29.609 23528 Z= 0.332 Chirality : 0.043 0.175 2623 Planarity : 0.004 0.051 2804 Dihedral : 17.211 79.133 2835 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.17 % Allowed : 17.65 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.19), residues: 1925 helix: 0.28 (0.22), residues: 603 sheet: -0.43 (0.24), residues: 474 loop : -1.28 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 5 TYR 0.023 0.001 TYR D 60 PHE 0.029 0.002 PHE A 753 TRP 0.012 0.001 TRP A 671 HIS 0.006 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (17195) covalent geometry : angle 0.64823 / 0.33 (23516) hydrogen bonds : bond 0.03810 / 2.48 ( 777) hydrogen bonds : angle 4.98187 / 3.45 ( 2113) metal coordination : bond 0.00396 / 0.20 ( 4) metal coordination : angle 12.93213 / 7.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.7169 (tp) cc_final: 0.6578 (pp) REVERT: A 154 ARG cc_start: 0.7554 (mtt90) cc_final: 0.5611 (mtt-85) REVERT: A 178 ARG cc_start: 0.4668 (OUTLIER) cc_final: 0.2516 (ttp-170) REVERT: A 405 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.5826 (mtt) REVERT: A 626 ASP cc_start: 0.6000 (p0) cc_final: 0.4628 (p0) REVERT: A 820 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.5772 (tpp) REVERT: A 831 MET cc_start: 0.7188 (tmm) cc_final: 0.6518 (tmm) REVERT: A 905 PHE cc_start: 0.4791 (m-80) cc_final: 0.4412 (m-10) REVERT: A 1197 MET cc_start: -0.0333 (mmt) cc_final: -0.4079 (ttp) REVERT: B 68 MET cc_start: 0.4908 (tmm) cc_final: 0.3531 (ptp) REVERT: B 199 MET cc_start: 0.5466 (tpt) cc_final: 0.4872 (tpt) REVERT: C 1 MET cc_start: 0.2790 (OUTLIER) cc_final: 0.2477 (tpt) REVERT: D 211 TYR cc_start: 0.7989 (m-80) cc_final: 0.7685 (m-80) outliers start: 37 outliers final: 27 residues processed: 219 average time/residue: 0.1173 time to fit residues: 39.8438 Evaluate side-chains 217 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: [162, 192, 147, 172, 84, 180, 119, 76, 99, 155, 101] chunk 162 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 chunk 147 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 155 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.4517 r_free = 0.4517 target = 0.190175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.156769 restraints weight = 27922.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.156348 restraints weight = 22875.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.157064 restraints weight = 18242.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.157564 restraints weight = 17074.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.157955 restraints weight = 15425.173| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17199 Z= 0.144 Angle : 0.721 28.853 23528 Z= 0.340 Chirality : 0.043 0.169 2623 Planarity : 0.004 0.047 2804 Dihedral : 17.194 79.156 2835 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.23 % Allowed : 17.42 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.19), residues: 1925 helix: 0.29 (0.22), residues: 603 sheet: -0.53 (0.24), residues: 494 loop : -1.27 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 64 TYR 0.020 0.001 TYR A 470 PHE 0.045 0.002 PHE A 552 TRP 0.009 0.001 TRP A 671 HIS 0.005 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (17195) covalent geometry : angle 0.66161 / 0.34 (23516) hydrogen bonds : bond 0.03898 / 2.53 ( 777) hydrogen bonds : angle 4.99244 / 3.46 ( 2113) metal coordination : bond 0.00502 / 0.26 ( 4) metal coordination : angle 12.67034 / 7.12 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.7254 (tp) cc_final: 0.6631 (pp) REVERT: A 154 ARG cc_start: 0.7579 (mtt90) cc_final: 0.5705 (mtt-85) REVERT: A 178 ARG cc_start: 0.4824 (OUTLIER) cc_final: 0.2572 (ttp-170) REVERT: A 405 MET cc_start: 0.5914 (OUTLIER) cc_final: 0.5683 (mtt) REVERT: A 626 ASP cc_start: 0.6100 (p0) cc_final: 0.5191 (p0) REVERT: A 639 ARG cc_start: 0.7038 (mmm-85) cc_final: 0.6775 (mmm-85) REVERT: A 820 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.5970 (tpp) REVERT: A 831 MET cc_start: 0.7244 (tmm) cc_final: 0.6565 (tmm) REVERT: A 1197 MET cc_start: -0.0376 (mmt) cc_final: -0.4177 (ttp) REVERT: B 199 MET cc_start: 0.5501 (tpt) cc_final: 0.4897 (tpt) REVERT: C 1 MET cc_start: 0.2854 (OUTLIER) cc_final: 0.2546 (tpt) REVERT: C 8 GLN cc_start: 0.7485 (pp30) cc_final: 0.6330 (pm20) REVERT: D 211 TYR cc_start: 0.8048 (m-80) cc_final: 0.7742 (m-80) outliers start: 38 outliers final: 30 residues processed: 210 average time/residue: 0.1210 time to fit residues: 39.1196 Evaluate side-chains 217 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: [147, 44, 79, 102, 22, 123, 110, 121, 176, 6, 179] chunk 147 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 110 optimal weight: 0.3980 chunk 121 optimal weight: 5.9990 chunk 176 optimal weight: 0.0370 chunk 6 optimal weight: 0.0470 chunk 179 optimal weight: 7.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- 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 = 0.4555 r_free = 0.4555 target = 0.193882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.162258 restraints weight = 26872.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.162139 restraints weight = 23505.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.162685 restraints weight = 18265.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.162904 restraints weight = 17601.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.163296 restraints weight = 16006.864| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17199 Z= 0.119 Angle : 0.701 25.780 23528 Z= 0.332 Chirality : 0.043 0.185 2623 Planarity : 0.004 0.049 2804 Dihedral : 17.153 79.707 2835 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.94 % Allowed : 17.89 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.19), residues: 1925 helix: 0.43 (0.22), residues: 597 sheet: -0.41 (0.24), residues: 478 loop : -1.17 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 762 TYR 0.019 0.001 TYR A 470 PHE 0.037 0.002 PHE A 552 TRP 0.018 0.001 TRP A 671 HIS 0.006 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (17195) covalent geometry : angle 0.64730 / 0.33 (23516) hydrogen bonds : bond 0.03651 / 2.39 ( 777) hydrogen bonds : angle 4.91372 / 3.39 ( 2113) metal coordination : bond 0.00398 / 0.20 ( 4) metal coordination : angle 11.97538 / 6.72 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2330.42 seconds wall clock time: 41 minutes 28.19 seconds (2488.19 seconds total)