Starting phenix.real_space_refine on Sat Oct 11 05:02:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v1s_42889/10_2025/8v1s_42889_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v1s_42889/10_2025/8v1s_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_42889/10_2025/8v1s_42889_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v1s_42889/10_2025/8v1s_42889_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v1s_42889/10_2025/8v1s_42889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v1s_42889/10_2025/8v1s_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-2.0-5842/lib/python3.9/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: 5.00, per 1000 atoms: 0.42 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: 1.10 Conformation dependent library (CDL) restraints added in 969.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.71 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: 2.82 Time building geometry restraints manager: 1.47 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=" 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 bond pdb=" CG LEU B 109 " pdb=" CD1 LEU B 109 " ideal model delta sigma weight residual 1.521 1.331 0.190 3.30e-02 9.18e+02 3.30e+01 bond pdb=" CB PRO B 132 " pdb=" CG PRO B 132 " ideal model delta sigma weight residual 1.492 1.241 0.251 5.00e-02 4.00e+02 2.52e+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: 1165 0.062 - 0.125: 531 0.125 - 0.187: 165 0.187 - 0.249: 33 0.249 - 0.311: 11 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.430 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 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= 0.795 Angle : 1.640 73.840 16898 Z= 0.892 Chirality : 0.078 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 aren 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 covalent geometry : bond 0.01831 (12274) covalent geometry : angle 1.64011 (16898) hydrogen bonds : bond 0.16013 ( 489) hydrogen bonds : angle 8.26753 ( 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 : 0.417 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: 0.1349 time to fit residues: 20.6734 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 : 0.429 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.172427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.147826 restraints weight = 55135.823| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 4.62 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 12274 Z= 0.224 Angle : 0.887 15.691 16898 Z= 0.475 Chirality : 0.052 0.240 1905 Planarity : 0.007 0.070 1975 Dihedral : 22.668 179.703 2150 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.75 % Favored : 92.88 % Rotamer: Outliers : 3.64 % Allowed : 28.04 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.21), residues: 1357 helix: -1.00 (0.22), residues: 451 sheet: -2.29 (0.32), residues: 223 loop : -2.60 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 558 TYR 0.021 0.002 TYR A1148 PHE 0.024 0.003 PHE A 733 TRP 0.025 0.003 TRP A 781 HIS 0.010 0.002 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00519 (12274) covalent geometry : angle 0.88698 (16898) hydrogen bonds : bond 0.05792 ( 489) hydrogen bonds : angle 6.24902 ( 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 182 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 PHE cc_start: 0.6610 (t80) cc_final: 0.6408 (t80) REVERT: A 451 MET cc_start: 0.7426 (mmm) cc_final: 0.7055 (mmm) REVERT: A 510 GLN cc_start: 0.5651 (OUTLIER) cc_final: 0.4209 (mt0) REVERT: A 756 GLU cc_start: 0.5829 (OUTLIER) cc_final: 0.5370 (mt-10) REVERT: B 61 MET cc_start: 0.7435 (mtt) cc_final: 0.7014 (mtp) outliers start: 39 outliers final: 17 residues processed: 171 average time/residue: 0.1228 time to fit residues: 30.0805 Evaluate side-chains 134 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 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 702 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU 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 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: 2.9990 chunk 72 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 HIS A 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.173154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.148676 restraints weight = 52299.533| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 4.63 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12274 Z= 0.202 Angle : 0.799 8.860 16898 Z= 0.426 Chirality : 0.050 0.267 1905 Planarity : 0.006 0.063 1975 Dihedral : 22.489 179.653 2150 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.45 % Favored : 93.40 % Rotamer: Outliers : 3.90 % Allowed : 26.89 % Favored : 69.21 % 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 aren not related in a simple way. whole: -2.39 (0.21), residues: 1357 helix: -0.59 (0.23), residues: 460 sheet: -1.79 (0.31), residues: 235 loop : -2.22 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 558 TYR 0.019 0.002 TYR A 281 PHE 0.021 0.002 PHE A 733 TRP 0.016 0.002 TRP A 781 HIS 0.008 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00467 (12274) covalent geometry : angle 0.79873 (16898) hydrogen bonds : bond 0.05141 ( 489) hydrogen bonds : angle 5.70196 ( 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 185 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.453 Fit side-chains REVERT: A 451 MET cc_start: 0.7881 (mmm) cc_final: 0.7444 (mmm) REVERT: A 510 GLN cc_start: 0.5394 (OUTLIER) cc_final: 0.4466 (mt0) REVERT: A 756 GLU cc_start: 0.5656 (OUTLIER) cc_final: 0.5186 (mt-10) REVERT: A 934 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6617 (tp) REVERT: A 950 MET cc_start: 0.7034 (tpp) cc_final: 0.6605 (tpp) REVERT: A 1054 VAL cc_start: 0.6072 (OUTLIER) cc_final: 0.5641 (m) REVERT: B 51 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7673 (mtt-85) outliers start: 42 outliers final: 22 residues processed: 170 average time/residue: 0.1266 time to fit residues: 30.4881 Evaluate side-chains 141 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 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 206 TYR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 346 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 756 GLU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 934 LEU 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 B residue 51 ARG 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: 4.9990 chunk 54 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.171329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.146890 restraints weight = 56997.610| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 5.07 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12274 Z= 0.222 Angle : 0.791 9.775 16898 Z= 0.419 Chirality : 0.049 0.265 1905 Planarity : 0.006 0.065 1975 Dihedral : 22.305 178.727 2150 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.90 % Favored : 93.03 % Rotamer: Outliers : 4.08 % Allowed : 26.89 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -2.12 (0.22), residues: 1357 helix: -0.49 (0.23), residues: 462 sheet: -1.58 (0.31), residues: 234 loop : -1.99 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 116 TYR 0.016 0.002 TYR A 818 PHE 0.026 0.002 PHE B 98 TRP 0.011 0.001 TRP A 856 HIS 0.006 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00515 (12274) covalent geometry : angle 0.79125 (16898) hydrogen bonds : bond 0.05088 ( 489) hydrogen bonds : angle 5.61872 ( 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 176 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 0.366 Fit side-chains REVERT: A 155 ASN cc_start: 0.7327 (OUTLIER) cc_final: 0.7058 (p0) REVERT: A 451 MET cc_start: 0.7906 (mmm) cc_final: 0.7522 (mmm) REVERT: A 510 GLN cc_start: 0.5561 (OUTLIER) cc_final: 0.4566 (mt0) REVERT: A 703 ASP cc_start: 0.7301 (p0) cc_final: 0.7065 (p0) REVERT: A 756 GLU cc_start: 0.5633 (OUTLIER) cc_final: 0.5124 (mt-10) REVERT: A 934 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6674 (tp) REVERT: A 950 MET cc_start: 0.6982 (tpp) cc_final: 0.6720 (tpp) REVERT: A 1054 VAL cc_start: 0.6030 (OUTLIER) cc_final: 0.5695 (m) REVERT: B 51 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7796 (mtt-85) REVERT: B 309 VAL cc_start: 0.6312 (OUTLIER) cc_final: 0.5678 (p) outliers start: 44 outliers final: 31 residues processed: 162 average time/residue: 0.1099 time to fit residues: 26.3040 Evaluate side-chains 161 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 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 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 825 HIS Chi-restraints excluded: chain A residue 934 LEU 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 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 77 VAL 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 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.173229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.150125 restraints weight = 42966.990| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.43 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.3028 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= 0.227 Angle : 0.784 9.826 16898 Z= 0.416 Chirality : 0.049 0.278 1905 Planarity : 0.006 0.064 1975 Dihedral : 22.179 175.866 2150 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.82 % Favored : 93.10 % 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 aren not related in a simple way. whole: -1.90 (0.22), residues: 1357 helix: -0.38 (0.23), residues: 458 sheet: -1.24 (0.32), residues: 231 loop : -1.88 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1019 TYR 0.022 0.002 TYR A 818 PHE 0.023 0.002 PHE B 98 TRP 0.011 0.002 TRP A 856 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00531 (12274) covalent geometry : angle 0.78373 (16898) hydrogen bonds : bond 0.05080 ( 489) hydrogen bonds : angle 5.61407 ( 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 174 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.5237 (mp) cc_final: 0.4946 (tp) REVERT: A 155 ASN cc_start: 0.7312 (OUTLIER) cc_final: 0.6942 (p0) REVERT: A 451 MET cc_start: 0.7781 (mmm) cc_final: 0.7368 (mmm) REVERT: A 510 GLN cc_start: 0.5552 (OUTLIER) cc_final: 0.4770 (mt0) REVERT: A 756 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.5041 (mt-10) REVERT: A 934 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6697 (tp) REVERT: A 981 ASP cc_start: 0.5619 (m-30) cc_final: 0.5241 (p0) REVERT: A 984 SER cc_start: 0.7313 (OUTLIER) cc_final: 0.6644 (p) REVERT: A 1054 VAL cc_start: 0.5911 (OUTLIER) cc_final: 0.5617 (m) REVERT: A 1197 HIS cc_start: 0.6466 (OUTLIER) cc_final: 0.6217 (p90) REVERT: A 1234 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6963 (mp) REVERT: B 51 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7494 (mtt-85) outliers start: 50 outliers final: 34 residues processed: 160 average time/residue: 0.1259 time to fit residues: 28.7966 Evaluate side-chains 159 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 256 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 498 VAL 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 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 825 HIS Chi-restraints excluded: chain A residue 903 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 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 A residue 1197 HIS Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 77 VAL 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 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.175254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.152598 restraints weight = 46532.662| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 3.50 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4066 r_free = 0.4066 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4066 r_free = 0.4066 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12274 Z= 0.181 Angle : 0.733 9.542 16898 Z= 0.390 Chirality : 0.047 0.290 1905 Planarity : 0.005 0.064 1975 Dihedral : 22.000 171.110 2150 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.88 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 : 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 aren not related in a simple way. whole: -1.73 (0.22), residues: 1357 helix: -0.20 (0.24), residues: 459 sheet: -1.19 (0.33), residues: 231 loop : -1.80 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 222 TYR 0.020 0.002 TYR A 818 PHE 0.021 0.002 PHE A 965 TRP 0.012 0.001 TRP A 856 HIS 0.005 0.001 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00421 (12274) covalent geometry : angle 0.73314 (16898) hydrogen bonds : bond 0.04657 ( 489) hydrogen bonds : angle 5.41072 ( 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 180 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 0.437 Fit side-chains REVERT: A 99 LEU cc_start: 0.5369 (mp) cc_final: 0.5079 (tp) REVERT: A 155 ASN cc_start: 0.7152 (OUTLIER) cc_final: 0.6899 (p0) REVERT: A 451 MET cc_start: 0.7813 (mmm) cc_final: 0.7424 (mmm) REVERT: A 510 GLN cc_start: 0.5173 (OUTLIER) cc_final: 0.4759 (mt0) REVERT: A 540 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7209 (tp) REVERT: A 703 ASP cc_start: 0.7045 (p0) cc_final: 0.6769 (p0) REVERT: A 756 GLU cc_start: 0.5514 (OUTLIER) cc_final: 0.4978 (mt-10) REVERT: A 872 MET cc_start: 0.6957 (ttm) cc_final: 0.6700 (ttm) REVERT: A 1086 THR cc_start: 0.7406 (p) cc_final: 0.7202 (t) REVERT: A 1197 HIS cc_start: 0.6510 (OUTLIER) cc_final: 0.6218 (p90) REVERT: B 51 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7497 (mtt-85) REVERT: B 309 VAL cc_start: 0.6223 (OUTLIER) cc_final: 0.5371 (p) outliers start: 50 outliers final: 30 residues processed: 167 average time/residue: 0.1218 time to fit residues: 29.4796 Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 215 HIS 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 498 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 VAL 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 825 HIS Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1045 THR 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 1197 HIS Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 77 VAL 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 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: 0.0970 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.0270 chunk 139 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.177718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.157852 restraints weight = 63545.254| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 4.32 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12274 Z= 0.161 Angle : 0.717 10.478 16898 Z= 0.380 Chirality : 0.046 0.255 1905 Planarity : 0.006 0.076 1975 Dihedral : 21.873 170.741 2150 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.68 % Favored : 93.25 % Rotamer: Outliers : 4.17 % Allowed : 27.60 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.22), residues: 1357 helix: -0.04 (0.24), residues: 461 sheet: -1.20 (0.33), residues: 225 loop : -1.75 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 222 TYR 0.019 0.001 TYR A1148 PHE 0.024 0.002 PHE A 965 TRP 0.013 0.001 TRP A 781 HIS 0.034 0.002 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00370 (12274) covalent geometry : angle 0.71749 (16898) hydrogen bonds : bond 0.04397 ( 489) hydrogen bonds : angle 5.26362 ( 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 165 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 0.442 Fit side-chains REVERT: A 99 LEU cc_start: 0.5180 (mp) cc_final: 0.4966 (tp) REVERT: A 155 ASN cc_start: 0.6960 (OUTLIER) cc_final: 0.6720 (p0) REVERT: A 451 MET cc_start: 0.7756 (mmm) cc_final: 0.7374 (mmm) REVERT: A 510 GLN cc_start: 0.5140 (OUTLIER) cc_final: 0.4919 (mt0) REVERT: A 540 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7116 (tp) REVERT: A 703 ASP cc_start: 0.6935 (p0) cc_final: 0.6636 (p0) REVERT: A 756 GLU cc_start: 0.5620 (OUTLIER) cc_final: 0.5129 (mt-10) REVERT: A 872 MET cc_start: 0.7012 (ttm) cc_final: 0.6784 (ttm) REVERT: A 1086 THR cc_start: 0.7525 (p) cc_final: 0.7322 (t) REVERT: A 1197 HIS cc_start: 0.6488 (OUTLIER) cc_final: 0.6208 (p90) REVERT: B 51 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7608 (mtt-85) REVERT: B 309 VAL cc_start: 0.6120 (OUTLIER) cc_final: 0.5492 (p) outliers start: 45 outliers final: 29 residues processed: 154 average time/residue: 0.1251 time to fit residues: 27.4973 Evaluate side-chains 146 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 540 LEU 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 825 HIS Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1045 THR 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 1197 HIS 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 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 29 optimal weight: 0.0980 chunk 90 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.179469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.157254 restraints weight = 51857.893| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 4.04 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4120 r_free = 0.4120 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4120 r_free = 0.4120 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12274 Z= 0.151 Angle : 0.697 9.184 16898 Z= 0.370 Chirality : 0.045 0.194 1905 Planarity : 0.005 0.065 1975 Dihedral : 21.742 175.722 2150 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 4.35 % Allowed : 27.15 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.23), residues: 1357 helix: 0.08 (0.24), residues: 462 sheet: -1.19 (0.32), residues: 226 loop : -1.65 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 222 TYR 0.016 0.002 TYR A 818 PHE 0.023 0.002 PHE A 965 TRP 0.012 0.001 TRP A 856 HIS 0.011 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00345 (12274) covalent geometry : angle 0.69698 (16898) hydrogen bonds : bond 0.04268 ( 489) hydrogen bonds : angle 5.20741 ( 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 178 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 0.446 Fit side-chains REVERT: A 155 ASN cc_start: 0.7108 (OUTLIER) cc_final: 0.6863 (p0) REVERT: A 222 ARG cc_start: 0.4673 (tpt90) cc_final: 0.3700 (tpt-90) REVERT: A 451 MET cc_start: 0.7768 (mmm) cc_final: 0.7447 (mmm) REVERT: A 557 TYR cc_start: 0.5997 (p90) cc_final: 0.5506 (p90) REVERT: A 703 ASP cc_start: 0.6902 (p0) cc_final: 0.6565 (p0) REVERT: A 756 GLU cc_start: 0.5548 (OUTLIER) cc_final: 0.5084 (mt-10) REVERT: A 872 MET cc_start: 0.6977 (ttm) cc_final: 0.6723 (ttm) REVERT: A 934 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6428 (tp) REVERT: A 1019 ARG cc_start: 0.6423 (ttp80) cc_final: 0.6223 (tmm160) REVERT: A 1197 HIS cc_start: 0.6487 (OUTLIER) cc_final: 0.6192 (p90) REVERT: B 51 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7636 (mtt-85) REVERT: B 134 ARG cc_start: 0.5570 (mtt180) cc_final: 0.5319 (ttt90) REVERT: B 309 VAL cc_start: 0.6043 (OUTLIER) cc_final: 0.5493 (p) outliers start: 47 outliers final: 31 residues processed: 165 average time/residue: 0.1239 time to fit residues: 29.2275 Evaluate side-chains 149 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 218 CYS 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 534 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 772 SER Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1045 THR 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 1197 HIS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASP 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 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 94 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.0270 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 HIS A1152 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.176069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.154066 restraints weight = 53169.005| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 4.22 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12274 Z= 0.198 Angle : 0.734 10.309 16898 Z= 0.388 Chirality : 0.047 0.197 1905 Planarity : 0.005 0.063 1975 Dihedral : 21.733 173.653 2150 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.90 % Favored : 93.03 % Rotamer: Outliers : 3.73 % Allowed : 28.39 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.23), residues: 1357 helix: -0.04 (0.24), residues: 459 sheet: -1.07 (0.33), residues: 231 loop : -1.68 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 90 TYR 0.024 0.002 TYR A 818 PHE 0.030 0.002 PHE A 965 TRP 0.010 0.001 TRP A 856 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00464 (12274) covalent geometry : angle 0.73355 (16898) hydrogen bonds : bond 0.04659 ( 489) hydrogen bonds : angle 5.33405 ( 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 162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.419 Fit side-chains REVERT: A 155 ASN cc_start: 0.7100 (OUTLIER) cc_final: 0.6841 (p0) REVERT: A 451 MET cc_start: 0.7866 (mmm) cc_final: 0.7529 (mmm) REVERT: A 703 ASP cc_start: 0.7011 (p0) cc_final: 0.6673 (p0) REVERT: A 756 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.5171 (mt-10) REVERT: A 872 MET cc_start: 0.6991 (ttm) cc_final: 0.6607 (ttm) REVERT: A 934 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6747 (tp) REVERT: A 1019 ARG cc_start: 0.6576 (ttp80) cc_final: 0.6324 (tmm160) REVERT: A 1197 HIS cc_start: 0.6480 (OUTLIER) cc_final: 0.6208 (p90) REVERT: B 134 ARG cc_start: 0.5627 (mtt180) cc_final: 0.5371 (ttt90) outliers start: 40 outliers final: 33 residues processed: 151 average time/residue: 0.1252 time to fit residues: 26.8229 Evaluate side-chains 151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 218 CYS 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 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 534 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 772 SER Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1045 THR 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 1197 HIS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 19 optimal weight: 1.9990 chunk 132 optimal weight: 0.0020 chunk 36 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 chunk 115 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.177654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.154294 restraints weight = 42145.568| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 3.55 r_work: 0.3841 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12274 Z= 0.162 Angle : 0.703 9.224 16898 Z= 0.372 Chirality : 0.046 0.190 1905 Planarity : 0.005 0.063 1975 Dihedral : 21.584 173.831 2150 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 3.90 % Allowed : 28.22 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.23), residues: 1357 helix: 0.08 (0.24), residues: 461 sheet: -1.05 (0.33), residues: 228 loop : -1.68 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 112 TYR 0.025 0.002 TYR A 272 PHE 0.030 0.002 PHE A 965 TRP 0.013 0.002 TRP A 856 HIS 0.004 0.001 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00374 (12274) covalent geometry : angle 0.70253 (16898) hydrogen bonds : bond 0.04256 ( 489) hydrogen bonds : angle 5.23893 ( 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 160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.435 Fit side-chains REVERT: A 155 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6930 (p0) REVERT: A 226 GLU cc_start: 0.5214 (tp30) cc_final: 0.4603 (mp0) REVERT: A 451 MET cc_start: 0.7577 (mmm) cc_final: 0.7250 (mmm) REVERT: A 703 ASP cc_start: 0.7231 (p0) cc_final: 0.6828 (p0) REVERT: A 756 GLU cc_start: 0.5492 (OUTLIER) cc_final: 0.5013 (mt-10) REVERT: A 872 MET cc_start: 0.6958 (ttm) cc_final: 0.6561 (ttm) REVERT: A 934 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6844 (tp) REVERT: A 1197 HIS cc_start: 0.6913 (OUTLIER) cc_final: 0.6500 (p90) REVERT: B 134 ARG cc_start: 0.5688 (mtt180) cc_final: 0.5111 (ttt90) REVERT: B 163 THR cc_start: 0.7672 (p) cc_final: 0.7438 (p) outliers start: 42 outliers final: 36 residues processed: 149 average time/residue: 0.1178 time to fit residues: 25.7401 Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 218 CYS 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 371 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 540 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 772 SER 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 903 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1045 THR 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 1197 HIS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASP 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 195 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR 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: 0.0670 chunk 86 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4396 r_free = 0.4396 target = 0.179332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.159056 restraints weight = 58616.761| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 4.02 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4148 r_free = 0.4148 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4148 r_free = 0.4148 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12274 Z= 0.151 Angle : 0.683 8.761 16898 Z= 0.361 Chirality : 0.045 0.180 1905 Planarity : 0.005 0.058 1975 Dihedral : 21.428 170.568 2150 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.28 % Allowed : 28.84 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.23), residues: 1357 helix: 0.23 (0.24), residues: 460 sheet: -1.01 (0.33), residues: 227 loop : -1.66 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 112 TYR 0.029 0.002 TYR A 272 PHE 0.029 0.002 PHE A 965 TRP 0.013 0.001 TRP A 856 HIS 0.008 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00346 (12274) covalent geometry : angle 0.68339 (16898) hydrogen bonds : bond 0.04116 ( 489) hydrogen bonds : angle 5.11803 ( 1363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2534.96 seconds wall clock time: 44 minutes 34.11 seconds (2674.11 seconds total)