Starting phenix.real_space_refine on Fri Jul 3 03:22:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v1s_42889/07_2026/8v1s_42889_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v1s_42889/07_2026/8v1s_42889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v1s_42889/07_2026/8v1s_42889_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v1s_42889/07_2026/8v1s_42889_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v1s_42889/07_2026/8v1s_42889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v1s_42889/07_2026/8v1s_42889.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 59 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7398 2.51 5 N 2106 2.21 5 O 2277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11889 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8602 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1091, 8582 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1091, 8582 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 3 bond proxies already assigned to first conformer: 8759 Chain: "B" Number of atoms: 2079 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2070 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 14, 'TRANS': 254} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2070 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 14, 'TRANS': 254} Chain breaks: 1 bond proxies already assigned to first conformer: 2098 Chain: "P" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 536 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "T" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 671 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 700 " occ=0.44 ... (20 atoms not shown) pdb=" NH2BARG A 700 " occ=0.56 residue: pdb=" N ALYS A1182 " occ=0.52 ... (16 atoms not shown) pdb=" NZ BLYS A1182 " occ=0.48 residue: pdb=" N ALYS B 105 " occ=0.43 ... (16 atoms not shown) pdb=" NZ BLYS B 105 " occ=0.57 Time building chain proxies: 4.54, per 1000 atoms: 0.38 Number of scatterers: 11889 At special positions: 0 Unit cell: (154.275, 115.5, 89.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 59 15.00 Mg 1 11.99 O 2277 8.00 N 2106 7.00 C 7398 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: 1.03 Conformation dependent library (CDL) restraints added in 937.6 milliseconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 38.7% alpha, 19.1% beta 12 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 168 through 175 removed outlier: 4.399A pdb=" N MET A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.702A pdb=" N ARG A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.611A pdb=" N PHE A 335 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.621A pdb=" N LEU A 350 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 430 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.705A pdb=" N ASP A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 559 through 567 removed outlier: 4.186A pdb=" N GLY A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 593 Processing helix chain 'A' and resid 593 through 606 removed outlier: 3.789A pdb=" N GLU A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 617 through 632 removed outlier: 4.293A pdb=" N VAL A 621 " --> pdb=" O GLN A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.843A pdb=" N ASP A 703 " --> pdb=" O AARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 772 through 790 Processing helix chain 'A' and resid 796 through 816 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 830 through 855 Processing helix chain 'A' and resid 858 through 866 Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'A' and resid 901 through 917 removed outlier: 3.790A pdb=" N LYS A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 980 Processing helix chain 'A' and resid 983 through 990 Processing helix chain 'A' and resid 996 through 1001 removed outlier: 4.268A pdb=" N ALA A1000 " --> pdb=" O GLU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1007 through 1023 removed outlier: 3.755A pdb=" N VAL A1013 " --> pdb=" O ALA A1009 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1014 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1059 Processing helix chain 'A' and resid 1082 through 1094 Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1145 through 1152 removed outlier: 3.646A pdb=" N HIS A1152 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1174 removed outlier: 3.872A pdb=" N TYR A1161 " --> pdb=" O ASN A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1178 removed outlier: 3.559A pdb=" N GLY A1178 " --> pdb=" O ALA A1175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1175 through 1178' Processing helix chain 'A' and resid 1180 through 1189 Processing helix chain 'A' and resid 1190 through 1192 No H-bonds generated for 'chain 'A' and resid 1190 through 1192' Processing helix chain 'A' and resid 1199 through 1209 removed outlier: 4.487A pdb=" N ARG A1205 " --> pdb=" O ASP A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1235 removed outlier: 3.735A pdb=" N THR A1223 " --> pdb=" O THR A1219 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A1224 " --> pdb=" O ALA A1220 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A1225 " --> pdb=" O GLU A1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.614A pdb=" N ALYS B 105 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 4.003A pdb=" N ARG B 113 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 273 through 281 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 removed outlier: 9.046A pdb=" N VAL A 436 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 409 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU A 438 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 411 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 440 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER A 413 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 406 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP A 400 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 392 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL A 391 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS A 372 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 113 removed outlier: 9.046A pdb=" N VAL A 436 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 409 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU A 438 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 411 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 440 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER A 413 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 406 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP A 400 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 392 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 156 Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 208 Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 Processing sheet with id=AA9, first strand: chain 'A' and resid 708 through 709 removed outlier: 3.821A pdb=" N LYS A 928 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR A 884 " --> pdb=" O PHE A 891 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU A 893 " --> pdb=" O ILE A 882 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 882 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 709 removed outlier: 6.580A pdb=" N VAL A 944 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 933 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 942 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 754 through 755 Processing sheet with id=AB3, first strand: chain 'A' and resid 1212 through 1215 Processing sheet with id=AB4, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.879A pdb=" N TRP B 141 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 123 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG B 139 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU B 125 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 137 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE B 127 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR B 135 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.879A pdb=" N TRP B 141 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 123 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG B 139 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU B 125 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 137 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE B 127 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR B 135 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.598A pdb=" N GLN B 76 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 255 through 257 removed outlier: 8.485A pdb=" N VAL B 256 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 222 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 200 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 265 " --> pdb=" O LEU B 204 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.07: 1 1.07 - 1.27: 1789 1.27 - 1.46: 5232 1.46 - 1.66: 5179 1.66 - 1.86: 73 Bond restraints: 12274 Sorted by residual: bond pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 1.473 1.863 -0.390 1.40e-02 5.10e+03 7.77e+02 bond pdb=" CG PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 1.503 0.867 0.636 3.40e-02 8.65e+02 3.50e+02 bond pdb=" C1' DT P -12 " pdb=" N1 DT P -12 " ideal model delta sigma weight residual 1.468 1.565 -0.097 1.40e-02 5.10e+03 4.85e+01 bond pdb=" C3' DG T 21 " pdb=" O3' DG T 21 " ideal model delta sigma weight residual 1.435 1.519 -0.084 1.30e-02 5.92e+03 4.22e+01 bond pdb=" CB ASN A 518 " pdb=" CG ASN A 518 " ideal model delta sigma weight residual 1.516 1.364 0.152 2.50e-02 1.60e+03 3.70e+01 ... (remaining 12269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 16893 14.77 - 29.54: 3 29.54 - 44.30: 1 44.30 - 59.07: 0 59.07 - 73.84: 1 Bond angle restraints: 16898 Sorted by residual: angle pdb=" CB PRO B 132 " pdb=" CG PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 106.10 179.94 -73.84 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO B 132 " pdb=" CD PRO B 132 " pdb=" CG PRO B 132 " ideal model delta sigma weight residual 103.20 72.74 30.46 1.50e+00 4.44e-01 4.12e+02 angle pdb=" CA PRO B 132 " pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 112.00 86.76 25.24 1.40e+00 5.10e-01 3.25e+02 angle pdb=" CA PRO B 132 " pdb=" CB PRO B 132 " pdb=" CG PRO B 132 " ideal model delta sigma weight residual 104.50 77.70 26.80 1.90e+00 2.77e-01 1.99e+02 angle pdb=" N PRO B 132 " pdb=" CA PRO B 132 " pdb=" C PRO B 132 " ideal model delta sigma weight residual 113.86 124.08 -10.22 1.25e+00 6.40e-01 6.68e+01 ... (remaining 16893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 6616 34.54 - 69.07: 531 69.07 - 103.61: 26 103.61 - 138.15: 1 138.15 - 172.68: 6 Dihedral angle restraints: 7180 sinusoidal: 3240 harmonic: 3940 Sorted by residual: dihedral pdb=" CA ALA A 220 " pdb=" C ALA A 220 " pdb=" N PRO A 221 " pdb=" CA PRO A 221 " ideal model delta harmonic sigma weight residual 180.00 -123.91 -56.09 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA GLY B 305 " pdb=" C GLY B 305 " pdb=" N PRO B 306 " pdb=" CA PRO B 306 " ideal model delta harmonic sigma weight residual -180.00 -125.50 -54.50 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA SER A1038 " pdb=" C SER A1038 " pdb=" N ARG A1039 " pdb=" CA ARG A1039 " ideal model delta harmonic sigma weight residual -180.00 -126.53 -53.47 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 7177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1144 0.062 - 0.125: 534 0.125 - 0.187: 176 0.187 - 0.249: 39 0.249 - 0.311: 12 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CB VAL B 212 " pdb=" CA VAL B 212 " pdb=" CG1 VAL B 212 " pdb=" CG2 VAL B 212 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB VAL A 253 " pdb=" CA VAL A 253 " pdb=" CG1 VAL A 253 " pdb=" CG2 VAL A 253 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASP B 146 " pdb=" N ASP B 146 " pdb=" C ASP B 146 " pdb=" CB ASP B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1902 not shown) Planarity restraints: 1975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 131 " 0.180 5.00e-02 4.00e+02 2.15e-01 7.42e+01 pdb=" N PRO B 132 " -0.368 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " 0.098 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 48 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO B 49 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 716 " -0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C PHE A 716 " 0.080 2.00e-02 2.50e+03 pdb=" O PHE A 716 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP A 717 " -0.027 2.00e-02 2.50e+03 ... (remaining 1972 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 88 2.45 - 3.06: 8441 3.06 - 3.68: 19079 3.68 - 4.29: 27983 4.29 - 4.90: 46522 Nonbonded interactions: 102113 Sorted by model distance: nonbonded pdb=" O LEU A 583 " pdb=" OE1 GLN A 587 " model vdw 1.841 3.040 nonbonded pdb=" OG1 THR A 312 " pdb=" O ALA A 602 " model vdw 1.933 3.040 nonbonded pdb=" OD2 ASP A 471 " pdb="MG MG A1301 " model vdw 1.970 2.170 nonbonded pdb=" OD1 ASP A 471 " pdb="MG MG A1301 " model vdw 1.973 2.170 nonbonded pdb=" OG SER A 127 " pdb=" O LEU A 129 " model vdw 1.974 3.040 ... (remaining 102108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.800 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.018 0.636 12274 Z= 0.881 Angle : 1.657 73.840 16898 Z= 0.957 Chirality : 0.081 0.311 1905 Planarity : 0.015 0.215 1975 Dihedral : 22.660 172.682 4648 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 0.30 % Favored : 99.55 % Rotamer: Outliers : 0.18 % Allowed : 31.32 % Favored : 68.50 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.93 % 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: -4.48 (0.19), residues: 1357 helix: -2.28 (0.20), residues: 440 sheet: -2.69 (0.31), residues: 224 loop : -3.62 (0.19), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 302 TYR 0.034 0.005 TYR A 490 PHE 0.043 0.005 PHE A 733 TRP 0.024 0.005 TRP A 502 HIS 0.025 0.004 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.01843 / 0.88 (12274) covalent geometry : angle 1.65749 / 0.96 (16898) hydrogen bonds : bond 0.16013 / 11.00 ( 489) hydrogen bonds : angle 8.26753 / 5.93 ( 1363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 281 TYR cc_start: 0.6443 (t80) cc_final: 0.6147 (t80) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1227 time to fit residues: 18.9311 Evaluate side-chains 100 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.171293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.147265 restraints weight = 54975.329| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 4.75 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3975 r_free = 0.3975 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3975 r_free = 0.3975 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12274 Z= 0.240 Angle : 0.966 18.346 16898 Z= 0.517 Chirality : 0.057 0.297 1905 Planarity : 0.008 0.090 1975 Dihedral : 22.898 174.361 2150 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.10 % Rotamer: Outliers : 3.64 % Allowed : 27.51 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.62 % 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: -3.18 (0.21), residues: 1357 helix: -1.24 (0.22), residues: 447 sheet: -2.35 (0.31), residues: 222 loop : -2.64 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 214 TYR 0.021 0.002 TYR A1148 PHE 0.034 0.003 PHE B 98 TRP 0.025 0.003 TRP A 781 HIS 0.008 0.002 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.24 (12274) covalent geometry : angle 0.96560 / 0.52 (16898) hydrogen bonds : bond 0.06497 / 4.37 ( 489) hydrogen bonds : angle 6.56175 / 4.78 ( 1363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7593 (mmm) cc_final: 0.7198 (mmm) REVERT: A 481 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7169 (p0) REVERT: A 615 ASP cc_start: 0.8040 (p0) cc_final: 0.7828 (p0) REVERT: A 756 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5523 (mt-10) outliers start: 39 outliers final: 18 residues processed: 157 average time/residue: 0.1048 time to fit residues: 23.8281 Evaluate side-chains 125 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.170925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.146153 restraints weight = 52314.510| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 4.42 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12274 Z= 0.233 Angle : 0.870 10.395 16898 Z= 0.466 Chirality : 0.055 0.367 1905 Planarity : 0.007 0.067 1975 Dihedral : 22.798 179.579 2150 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.31 % Favored : 93.55 % Rotamer: Outliers : 3.90 % Allowed : 27.51 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.31 % 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: -2.70 (0.21), residues: 1357 helix: -0.84 (0.22), residues: 449 sheet: -1.95 (0.32), residues: 217 loop : -2.42 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 214 TYR 0.034 0.003 TYR A 557 PHE 0.025 0.003 PHE B 98 TRP 0.019 0.002 TRP A 502 HIS 0.007 0.002 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 (12274) covalent geometry : angle 0.86978 / 0.47 (16898) hydrogen bonds : bond 0.05936 / 4.01 ( 489) hydrogen bonds : angle 6.08664 / 4.41 ( 1363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 427 LEU cc_start: 0.7559 (mp) cc_final: 0.7240 (mt) REVERT: A 451 MET cc_start: 0.7930 (mmm) cc_final: 0.7454 (mmm) REVERT: A 510 GLN cc_start: 0.5783 (OUTLIER) cc_final: 0.4497 (mt0) REVERT: A 615 ASP cc_start: 0.8014 (p0) cc_final: 0.7789 (p0) REVERT: A 756 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.5261 (mt-10) REVERT: A 950 MET cc_start: 0.7134 (tpp) cc_final: 0.6663 (tpp) REVERT: B 51 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7856 (mtt-85) outliers start: 42 outliers final: 28 residues processed: 159 average time/residue: 0.1100 time to fit residues: 25.8393 Evaluate side-chains 139 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 0.0470 chunk 134 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 HIS A 806 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.172748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.148142 restraints weight = 54340.609| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 4.62 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3983 r_free = 0.3983 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3983 r_free = 0.3983 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12274 Z= 0.189 Angle : 0.805 9.962 16898 Z= 0.430 Chirality : 0.053 0.302 1905 Planarity : 0.006 0.068 1975 Dihedral : 22.690 178.500 2150 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.97 % Favored : 92.95 % Rotamer: Outliers : 4.61 % Allowed : 27.33 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.31 % 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: -2.27 (0.22), residues: 1357 helix: -0.56 (0.23), residues: 459 sheet: -1.77 (0.31), residues: 233 loop : -2.08 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 214 TYR 0.026 0.002 TYR A 67 PHE 0.032 0.002 PHE A 313 TRP 0.017 0.002 TRP A 781 HIS 0.006 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (12274) covalent geometry : angle 0.80472 / 0.43 (16898) hydrogen bonds : bond 0.05244 / 3.53 ( 489) hydrogen bonds : angle 5.74098 / 4.14 ( 1363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 0.391 Fit side-chains REVERT: A 155 ASN cc_start: 0.7324 (OUTLIER) cc_final: 0.7093 (p0) REVERT: A 427 LEU cc_start: 0.7625 (mp) cc_final: 0.7277 (mt) REVERT: A 451 MET cc_start: 0.7838 (mmm) cc_final: 0.7427 (mmm) REVERT: A 510 GLN cc_start: 0.5550 (OUTLIER) cc_final: 0.4446 (mt0) REVERT: A 756 GLU cc_start: 0.5718 (OUTLIER) cc_final: 0.5236 (mt-10) REVERT: A 950 MET cc_start: 0.7123 (tpp) cc_final: 0.6705 (tpp) REVERT: B 51 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7405 (mtt-85) REVERT: B 309 VAL cc_start: 0.6157 (OUTLIER) cc_final: 0.5139 (p) outliers start: 50 outliers final: 30 residues processed: 164 average time/residue: 0.1155 time to fit residues: 27.4343 Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 136 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 chunk 29 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.172701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.148210 restraints weight = 42005.084| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.33 r_work: 0.3758 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12274 Z= 0.192 Angle : 0.785 10.480 16898 Z= 0.417 Chirality : 0.051 0.293 1905 Planarity : 0.006 0.070 1975 Dihedral : 22.594 173.804 2150 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 4.61 % Allowed : 27.06 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.31 % 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: -2.04 (0.22), residues: 1357 helix: -0.39 (0.23), residues: 460 sheet: -1.58 (0.31), residues: 230 loop : -1.94 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 222 TYR 0.023 0.002 TYR A 399 PHE 0.021 0.002 PHE A 313 TRP 0.010 0.001 TRP A 856 HIS 0.007 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (12274) covalent geometry : angle 0.78487 / 0.42 (16898) hydrogen bonds : bond 0.05109 / 3.46 ( 489) hydrogen bonds : angle 5.62461 / 4.05 ( 1363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 0.508 Fit side-chains REVERT: A 155 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7080 (p0) REVERT: A 427 LEU cc_start: 0.7760 (mp) cc_final: 0.7166 (mt) REVERT: A 451 MET cc_start: 0.7696 (mmm) cc_final: 0.7340 (mmm) REVERT: A 510 GLN cc_start: 0.5237 (OUTLIER) cc_final: 0.4254 (mt0) REVERT: A 515 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8478 (tt) REVERT: A 756 GLU cc_start: 0.5593 (OUTLIER) cc_final: 0.5122 (mt-10) REVERT: A 950 MET cc_start: 0.7216 (tpp) cc_final: 0.6886 (tpp) REVERT: A 1054 VAL cc_start: 0.6223 (OUTLIER) cc_final: 0.5823 (m) REVERT: B 51 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7735 (mtt-85) REVERT: B 309 VAL cc_start: 0.6836 (OUTLIER) cc_final: 0.5946 (p) outliers start: 50 outliers final: 35 residues processed: 163 average time/residue: 0.1138 time to fit residues: 27.1813 Evaluate side-chains 153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 6.9990 chunk 138 optimal weight: 40.0000 chunk 128 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A1157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.173522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.149860 restraints weight = 46583.341| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 4.28 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12274 Z= 0.173 Angle : 0.766 9.516 16898 Z= 0.406 Chirality : 0.050 0.286 1905 Planarity : 0.006 0.125 1975 Dihedral : 22.468 172.952 2150 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 4.61 % Allowed : 27.60 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.23 % 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: -1.87 (0.22), residues: 1357 helix: -0.25 (0.24), residues: 460 sheet: -1.52 (0.31), residues: 228 loop : -1.83 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 222 TYR 0.022 0.002 TYR A 818 PHE 0.019 0.002 PHE A 313 TRP 0.011 0.001 TRP A 781 HIS 0.020 0.002 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (12274) covalent geometry : angle 0.76589 / 0.41 (16898) hydrogen bonds : bond 0.04889 / 3.30 ( 489) hydrogen bonds : angle 5.51576 / 3.97 ( 1363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 0.522 Fit side-chains REVERT: A 155 ASN cc_start: 0.7183 (OUTLIER) cc_final: 0.6929 (p0) REVERT: A 451 MET cc_start: 0.7972 (mmm) cc_final: 0.7553 (mmm) REVERT: A 510 GLN cc_start: 0.5426 (OUTLIER) cc_final: 0.4552 (mt0) REVERT: A 515 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8395 (tt) REVERT: A 756 GLU cc_start: 0.5656 (OUTLIER) cc_final: 0.5160 (mt-10) REVERT: A 934 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6659 (tp) REVERT: A 981 ASP cc_start: 0.5601 (m-30) cc_final: 0.5126 (p0) REVERT: A 1054 VAL cc_start: 0.6077 (OUTLIER) cc_final: 0.5692 (m) REVERT: B 51 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7518 (mtt-85) REVERT: B 309 VAL cc_start: 0.6111 (OUTLIER) cc_final: 0.5231 (p) outliers start: 50 outliers final: 35 residues processed: 158 average time/residue: 0.1069 time to fit residues: 25.1036 Evaluate side-chains 160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A1157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.173700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.149906 restraints weight = 63244.871| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 5.26 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12274 Z= 0.172 Angle : 0.755 10.515 16898 Z= 0.399 Chirality : 0.050 0.278 1905 Planarity : 0.006 0.111 1975 Dihedral : 22.339 173.196 2150 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 4.88 % Allowed : 26.97 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.23 % 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: -1.74 (0.22), residues: 1357 helix: -0.13 (0.24), residues: 458 sheet: -1.35 (0.31), residues: 231 loop : -1.80 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 222 TYR 0.020 0.002 TYR A 818 PHE 0.019 0.002 PHE A 965 TRP 0.011 0.001 TRP A 856 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (12274) covalent geometry : angle 0.75549 / 0.40 (16898) hydrogen bonds : bond 0.04763 / 3.21 ( 489) hydrogen bonds : angle 5.44114 / 3.90 ( 1363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 0.476 Fit side-chains REVERT: A 99 LEU cc_start: 0.5295 (mp) cc_final: 0.4972 (tp) REVERT: A 155 ASN cc_start: 0.7198 (OUTLIER) cc_final: 0.6946 (p0) REVERT: A 451 MET cc_start: 0.7864 (mmm) cc_final: 0.7480 (mmm) REVERT: A 510 GLN cc_start: 0.5250 (OUTLIER) cc_final: 0.4562 (mt0) REVERT: A 515 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8470 (tt) REVERT: A 756 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.5115 (mt-10) REVERT: A 934 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6621 (tp) REVERT: A 981 ASP cc_start: 0.5547 (m-30) cc_final: 0.5117 (p0) REVERT: B 51 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7851 (mtt-85) REVERT: B 134 ARG cc_start: 0.5621 (ttt180) cc_final: 0.5108 (ttt90) REVERT: B 309 VAL cc_start: 0.5950 (OUTLIER) cc_final: 0.5305 (p) outliers start: 53 outliers final: 40 residues processed: 161 average time/residue: 0.1200 time to fit residues: 27.7024 Evaluate side-chains 161 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 114 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 HIS A1157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.177710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.156156 restraints weight = 51341.117| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 3.71 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4112 r_free = 0.4112 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4112 r_free = 0.4112 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12274 Z= 0.160 Angle : 0.750 9.332 16898 Z= 0.395 Chirality : 0.049 0.279 1905 Planarity : 0.006 0.108 1975 Dihedral : 22.242 172.954 2150 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 4.44 % Allowed : 27.68 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.23 % 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: -1.59 (0.22), residues: 1357 helix: -0.03 (0.24), residues: 459 sheet: -1.27 (0.31), residues: 228 loop : -1.69 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 222 TYR 0.019 0.002 TYR A 818 PHE 0.022 0.002 PHE A 965 TRP 0.011 0.001 TRP A 856 HIS 0.025 0.002 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (12274) covalent geometry : angle 0.75048 / 0.40 (16898) hydrogen bonds : bond 0.04629 / 3.12 ( 489) hydrogen bonds : angle 5.36552 / 3.83 ( 1363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 121 time to evaluate : 0.447 Fit side-chains REVERT: A 99 LEU cc_start: 0.5399 (mp) cc_final: 0.5145 (tp) REVERT: A 155 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6813 (p0) REVERT: A 451 MET cc_start: 0.7793 (mmm) cc_final: 0.7412 (mmm) REVERT: A 510 GLN cc_start: 0.5146 (OUTLIER) cc_final: 0.4782 (mt0) REVERT: A 756 GLU cc_start: 0.5617 (OUTLIER) cc_final: 0.5132 (mt-10) REVERT: A 934 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6668 (tp) REVERT: A 984 SER cc_start: 0.7266 (OUTLIER) cc_final: 0.6525 (p) REVERT: A 1054 VAL cc_start: 0.5877 (OUTLIER) cc_final: 0.5592 (m) REVERT: B 51 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7391 (mtt-85) REVERT: B 134 ARG cc_start: 0.5472 (ttt180) cc_final: 0.5129 (ttt90) REVERT: B 309 VAL cc_start: 0.6040 (OUTLIER) cc_final: 0.5145 (p) outliers start: 48 outliers final: 35 residues processed: 155 average time/residue: 0.1240 time to fit residues: 27.2650 Evaluate side-chains 158 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 94 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 729 HIS A1157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.176264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.154594 restraints weight = 53087.646| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 3.93 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12274 Z= 0.184 Angle : 0.755 9.656 16898 Z= 0.398 Chirality : 0.050 0.281 1905 Planarity : 0.006 0.103 1975 Dihedral : 22.179 173.582 2150 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 4.88 % Allowed : 27.42 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.58 (0.23), residues: 1357 helix: -0.05 (0.24), residues: 459 sheet: -1.20 (0.32), residues: 232 loop : -1.69 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 255 TYR 0.024 0.002 TYR A1148 PHE 0.020 0.002 PHE A 965 TRP 0.011 0.001 TRP A 856 HIS 0.009 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (12274) covalent geometry : angle 0.75514 / 0.40 (16898) hydrogen bonds : bond 0.04727 / 3.20 ( 489) hydrogen bonds : angle 5.37209 / 3.84 ( 1363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 0.445 Fit side-chains REVERT: A 99 LEU cc_start: 0.5521 (mp) cc_final: 0.5216 (tp) REVERT: A 155 ASN cc_start: 0.7115 (OUTLIER) cc_final: 0.6842 (p0) REVERT: A 451 MET cc_start: 0.7842 (mmm) cc_final: 0.7493 (mmm) REVERT: A 510 GLN cc_start: 0.5197 (OUTLIER) cc_final: 0.4819 (mt0) REVERT: A 615 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7760 (p0) REVERT: A 756 GLU cc_start: 0.5672 (OUTLIER) cc_final: 0.5176 (mt-10) REVERT: A 934 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6683 (tp) REVERT: A 984 SER cc_start: 0.7141 (OUTLIER) cc_final: 0.6434 (p) REVERT: A 1054 VAL cc_start: 0.5917 (OUTLIER) cc_final: 0.5626 (m) REVERT: A 1086 THR cc_start: 0.7544 (p) cc_final: 0.7280 (t) REVERT: B 134 ARG cc_start: 0.5426 (ttt180) cc_final: 0.5104 (ttt90) outliers start: 53 outliers final: 43 residues processed: 154 average time/residue: 0.1130 time to fit residues: 25.4302 Evaluate side-chains 159 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 19 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.174717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.151588 restraints weight = 41194.820| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.27 r_work: 0.3805 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12274 Z= 0.229 Angle : 0.791 10.419 16898 Z= 0.417 Chirality : 0.051 0.278 1905 Planarity : 0.006 0.107 1975 Dihedral : 22.180 174.162 2150 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.75 % Favored : 93.18 % Rotamer: Outliers : 4.61 % Allowed : 27.33 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.66 (0.22), residues: 1357 helix: -0.16 (0.24), residues: 458 sheet: -1.17 (0.33), residues: 230 loop : -1.73 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 222 TYR 0.026 0.002 TYR A 259 PHE 0.020 0.003 PHE A 965 TRP 0.015 0.002 TRP A 856 HIS 0.023 0.002 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (12274) covalent geometry : angle 0.79071 / 0.42 (16898) hydrogen bonds : bond 0.04961 / 3.38 ( 489) hydrogen bonds : angle 5.50122 / 3.90 ( 1363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 0.432 Fit side-chains REVERT: A 99 LEU cc_start: 0.5757 (mp) cc_final: 0.5409 (tp) REVERT: A 155 ASN cc_start: 0.7259 (OUTLIER) cc_final: 0.6959 (p0) REVERT: A 451 MET cc_start: 0.7668 (mmm) cc_final: 0.7331 (mmm) REVERT: A 510 GLN cc_start: 0.4906 (OUTLIER) cc_final: 0.4450 (mt0) REVERT: A 756 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.5019 (mt-10) REVERT: A 934 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6904 (tp) REVERT: A 984 SER cc_start: 0.7339 (OUTLIER) cc_final: 0.6623 (p) REVERT: A 1054 VAL cc_start: 0.6246 (OUTLIER) cc_final: 0.5953 (m) REVERT: B 134 ARG cc_start: 0.5752 (ttt180) cc_final: 0.5156 (ttt90) outliers start: 50 outliers final: 43 residues processed: 149 average time/residue: 0.1144 time to fit residues: 25.0343 Evaluate side-chains 162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 89 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 135 optimal weight: 40.0000 chunk 80 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 912 HIS A1157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.177002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.155794 restraints weight = 57953.164| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 4.31 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12274 Z= 0.165 Angle : 0.752 9.213 16898 Z= 0.398 Chirality : 0.050 0.280 1905 Planarity : 0.006 0.088 1975 Dihedral : 22.107 173.243 2150 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.35 % Allowed : 27.51 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.60 (0.23), residues: 1357 helix: -0.06 (0.24), residues: 458 sheet: -1.25 (0.33), residues: 227 loop : -1.69 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 222 TYR 0.025 0.002 TYR A1148 PHE 0.020 0.002 PHE A 965 TRP 0.015 0.002 TRP A 856 HIS 0.027 0.002 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (12274) covalent geometry : angle 0.75213 / 0.40 (16898) hydrogen bonds : bond 0.04638 / 3.13 ( 489) hydrogen bonds : angle 5.40885 / 3.84 ( 1363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.77 seconds wall clock time: 44 minutes 54.41 seconds (2694.41 seconds total)