Starting phenix.real_space_refine on Wed Jul 30 01:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v1s_42889/07_2025/8v1s_42889_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v1s_42889/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v1s_42889/07_2025/8v1s_42889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v1s_42889/07_2025/8v1s_42889.map" model { file = "/net/cci-nas-00/data/ceres_data/8v1s_42889/07_2025/8v1s_42889_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v1s_42889/07_2025/8v1s_42889_neut.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.87, per 1000 atoms: 1.00 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: 2.98 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 4.42 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: 5.30 Time building geometry restraints manager: 3.56 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: 1.690 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 40.080 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.640 ------------------------------------------------------------------------------- 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 : 11.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.005 TRP A 502 HIS 0.025 0.004 HIS A 192 PHE 0.043 0.005 PHE A 733 TYR 0.034 0.005 TYR A 490 ARG 0.025 0.001 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.16013 ( 489) hydrogen bonds : angle 8.26753 ( 1363) covalent geometry : bond 0.01831 (12274) covalent geometry : angle 1.64011 (16898) *********************** 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 : 1.213 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: 0.2854 time to fit residues: 43.8449 Evaluate side-chains 99 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.173421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.149579 restraints weight = 47837.389| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.81 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 12274 Z= 0.214 Angle : 0.879 16.997 16898 Z= 0.471 Chirality : 0.051 0.235 1905 Planarity : 0.007 0.073 1975 Dihedral : 22.634 179.105 2150 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.75 % Favored : 92.88 % Rotamer: Outliers : 3.64 % Allowed : 27.51 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.21), residues: 1357 helix: -0.98 (0.22), residues: 453 sheet: -2.29 (0.32), residues: 223 loop : -2.61 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 781 HIS 0.009 0.002 HIS A 192 PHE 0.022 0.003 PHE A 240 TYR 0.021 0.002 TYR A1148 ARG 0.008 0.001 ARG A 558 Details of bonding type rmsd hydrogen bonds : bond 0.05712 ( 489) hydrogen bonds : angle 6.19621 ( 1363) covalent geometry : bond 0.00489 (12274) covalent geometry : angle 0.87913 (16898) *********************** 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 186 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 TYR cc_start: 0.6473 (t80) cc_final: 0.6269 (t80) REVERT: A 365 MET cc_start: 0.7484 (ttp) cc_final: 0.7270 (ttp) REVERT: A 451 MET cc_start: 0.7290 (mmm) cc_final: 0.6940 (mmm) REVERT: A 510 GLN cc_start: 0.5656 (OUTLIER) cc_final: 0.4399 (mt0) REVERT: A 615 ASP cc_start: 0.8067 (p0) cc_final: 0.7865 (p0) REVERT: A 756 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5221 (mt-10) REVERT: B 61 MET cc_start: 0.7510 (mtt) cc_final: 0.7055 (mtp) outliers start: 39 outliers final: 15 residues processed: 174 average time/residue: 0.2488 time to fit residues: 62.7554 Evaluate side-chains 129 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 102 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.172130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.148102 restraints weight = 42375.299| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.58 r_work: 0.3726 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12274 Z= 0.221 Angle : 0.812 8.881 16898 Z= 0.433 Chirality : 0.050 0.263 1905 Planarity : 0.006 0.066 1975 Dihedral : 22.506 178.364 2150 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.10 % Rotamer: Outliers : 3.37 % Allowed : 27.24 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.21), residues: 1357 helix: -0.73 (0.22), residues: 462 sheet: -1.90 (0.31), residues: 234 loop : -2.26 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 856 HIS 0.008 0.001 HIS A 192 PHE 0.026 0.002 PHE A 313 TYR 0.018 0.002 TYR A1148 ARG 0.007 0.001 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.05258 ( 489) hydrogen bonds : angle 5.82616 ( 1363) covalent geometry : bond 0.00517 (12274) covalent geometry : angle 0.81191 (16898) *********************** 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 166 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 281 TYR cc_start: 0.6706 (t80) cc_final: 0.6277 (t80) REVERT: A 451 MET cc_start: 0.7711 (mmm) cc_final: 0.7417 (mmm) REVERT: A 510 GLN cc_start: 0.5100 (OUTLIER) cc_final: 0.4064 (mt0) REVERT: A 615 ASP cc_start: 0.8267 (p0) cc_final: 0.8021 (p0) REVERT: A 756 GLU cc_start: 0.5643 (OUTLIER) cc_final: 0.5214 (mt-10) REVERT: A 950 MET cc_start: 0.7167 (tpp) cc_final: 0.6712 (tpp) REVERT: A 1054 VAL cc_start: 0.6253 (OUTLIER) cc_final: 0.5825 (m) REVERT: B 51 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7761 (mtt-85) outliers start: 36 outliers final: 20 residues processed: 154 average time/residue: 0.2492 time to fit residues: 55.0807 Evaluate side-chains 136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 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 733 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 825 HIS 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 138 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 323 ASN A 806 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.171930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.147633 restraints weight = 47292.532| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 4.29 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12274 Z= 0.209 Angle : 0.778 9.508 16898 Z= 0.413 Chirality : 0.049 0.264 1905 Planarity : 0.006 0.065 1975 Dihedral : 22.291 178.248 2150 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 4.44 % Allowed : 25.91 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.22), residues: 1357 helix: -0.55 (0.23), residues: 463 sheet: -1.68 (0.30), residues: 234 loop : -2.00 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 856 HIS 0.006 0.001 HIS A 192 PHE 0.051 0.002 PHE A 313 TYR 0.016 0.002 TYR A 818 ARG 0.007 0.001 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 489) hydrogen bonds : angle 5.63626 ( 1363) covalent geometry : bond 0.00487 (12274) covalent geometry : angle 0.77794 (16898) *********************** 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 185 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.7262 (p0) REVERT: A 281 TYR cc_start: 0.6540 (t80) cc_final: 0.6193 (t80) REVERT: A 365 MET cc_start: 0.7381 (ttp) cc_final: 0.7166 (ttp) REVERT: A 451 MET cc_start: 0.7926 (mmm) cc_final: 0.7556 (mmm) REVERT: A 510 GLN cc_start: 0.5512 (OUTLIER) cc_final: 0.4550 (mt0) REVERT: A 540 LEU cc_start: 0.7705 (tp) cc_final: 0.7400 (tp) REVERT: A 703 ASP cc_start: 0.7248 (p0) cc_final: 0.7009 (p0) REVERT: A 756 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.5083 (mt-10) REVERT: A 934 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6648 (tp) REVERT: A 950 MET cc_start: 0.7102 (tpp) cc_final: 0.6736 (tpp) REVERT: A 1054 VAL cc_start: 0.6058 (OUTLIER) cc_final: 0.5707 (m) REVERT: B 51 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7622 (mtt-85) REVERT: B 309 VAL cc_start: 0.6300 (OUTLIER) cc_final: 0.5464 (p) outliers start: 48 outliers final: 31 residues processed: 171 average time/residue: 0.2451 time to fit residues: 60.2496 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 : 1.213 ------------------------------------------------------------------------------- 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 178 THR 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 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 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 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 B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 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 63 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 0.0000 chunk 92 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 A1157 ASN A1164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.178073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.157155 restraints weight = 43551.190| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.46 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12274 Z= 0.162 Angle : 0.721 9.181 16898 Z= 0.384 Chirality : 0.046 0.206 1905 Planarity : 0.005 0.064 1975 Dihedral : 21.987 170.415 2150 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 3.46 % Allowed : 27.68 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.22), residues: 1357 helix: -0.19 (0.24), residues: 460 sheet: -1.51 (0.31), residues: 229 loop : -1.79 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 856 HIS 0.005 0.001 HIS A 709 PHE 0.029 0.002 PHE A 313 TYR 0.020 0.002 TYR A1148 ARG 0.008 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 489) hydrogen bonds : angle 5.37900 ( 1363) covalent geometry : bond 0.00370 (12274) covalent geometry : angle 0.72082 (16898) *********************** 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 173 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.123 Fit side-chains REVERT: A 155 ASN cc_start: 0.7299 (OUTLIER) cc_final: 0.6995 (p0) REVERT: A 451 MET cc_start: 0.7675 (mmm) cc_final: 0.7270 (mmm) REVERT: A 510 GLN cc_start: 0.5107 (OUTLIER) cc_final: 0.4657 (mt0) REVERT: A 540 LEU cc_start: 0.7458 (tp) cc_final: 0.7020 (tp) REVERT: A 703 ASP cc_start: 0.6871 (p0) cc_final: 0.6556 (p0) REVERT: A 756 GLU cc_start: 0.5498 (OUTLIER) cc_final: 0.5028 (mt-10) REVERT: A 934 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6386 (tp) REVERT: A 950 MET cc_start: 0.6813 (tpp) cc_final: 0.6527 (tpp) REVERT: A 981 ASP cc_start: 0.5173 (m-30) cc_final: 0.4963 (p0) REVERT: A 1197 HIS cc_start: 0.6488 (OUTLIER) cc_final: 0.6222 (p90) REVERT: B 51 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7601 (mtt-85) REVERT: B 309 VAL cc_start: 0.5859 (OUTLIER) cc_final: 0.5240 (p) outliers start: 37 outliers final: 23 residues processed: 163 average time/residue: 0.2614 time to fit residues: 60.3108 Evaluate side-chains 143 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 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 346 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 543 VAL 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 825 HIS 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 1197 HIS Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 123 optimal weight: 0.1980 chunk 88 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS ** A 853 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 = 0.4385 r_free = 0.4385 target = 0.178357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.155675 restraints weight = 43832.220| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.27 r_work: 0.3872 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12274 Z= 0.159 Angle : 0.716 8.908 16898 Z= 0.380 Chirality : 0.047 0.352 1905 Planarity : 0.005 0.075 1975 Dihedral : 21.840 170.270 2150 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 3.99 % Allowed : 27.77 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.23), residues: 1357 helix: 0.02 (0.24), residues: 459 sheet: -1.43 (0.31), residues: 231 loop : -1.74 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 856 HIS 0.004 0.001 HIS A 709 PHE 0.024 0.002 PHE A 313 TYR 0.024 0.002 TYR A 818 ARG 0.012 0.001 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 489) hydrogen bonds : angle 5.24894 ( 1363) covalent geometry : bond 0.00366 (12274) covalent geometry : angle 0.71604 (16898) *********************** 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 170 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.7312 (OUTLIER) cc_final: 0.6988 (p0) REVERT: A 255 ARG cc_start: 0.6764 (mmm-85) cc_final: 0.6562 (mmm-85) REVERT: A 451 MET cc_start: 0.7467 (mmm) cc_final: 0.7116 (mmm) REVERT: A 510 GLN cc_start: 0.4651 (OUTLIER) cc_final: 0.4357 (mt0) REVERT: A 540 LEU cc_start: 0.7982 (tp) cc_final: 0.7531 (tp) REVERT: A 557 TYR cc_start: 0.6380 (p90) cc_final: 0.5855 (p90) REVERT: A 703 ASP cc_start: 0.7185 (p0) cc_final: 0.6815 (p0) REVERT: A 756 GLU cc_start: 0.5483 (OUTLIER) cc_final: 0.5032 (mt-10) REVERT: A 934 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6599 (tp) REVERT: A 981 ASP cc_start: 0.5349 (m-30) cc_final: 0.4995 (p0) REVERT: A 1054 VAL cc_start: 0.6115 (OUTLIER) cc_final: 0.5913 (m) REVERT: A 1234 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6902 (mp) REVERT: B 51 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7804 (mtt-85) REVERT: B 265 PHE cc_start: 0.5598 (p90) cc_final: 0.5349 (p90) REVERT: B 309 VAL cc_start: 0.6861 (OUTLIER) cc_final: 0.6157 (p) outliers start: 43 outliers final: 27 residues processed: 161 average time/residue: 0.3398 time to fit residues: 77.8960 Evaluate side-chains 149 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 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 543 VAL 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 1234 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 14 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 729 HIS ** A 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.177569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.156223 restraints weight = 61293.224| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 4.49 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4111 r_free = 0.4111 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4111 r_free = 0.4111 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12274 Z= 0.172 Angle : 0.716 9.513 16898 Z= 0.380 Chirality : 0.046 0.195 1905 Planarity : 0.005 0.061 1975 Dihedral : 21.788 170.486 2150 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.69 % Rotamer: Outliers : 3.99 % Allowed : 28.22 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.22), residues: 1357 helix: 0.03 (0.24), residues: 460 sheet: -1.40 (0.31), residues: 228 loop : -1.73 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 856 HIS 0.035 0.002 HIS A 215 PHE 0.022 0.002 PHE A 965 TYR 0.023 0.002 TYR A 851 ARG 0.007 0.001 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 489) hydrogen bonds : angle 5.26016 ( 1363) covalent geometry : bond 0.00398 (12274) covalent geometry : angle 0.71563 (16898) *********************** 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 163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 2.190 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.7119 (OUTLIER) cc_final: 0.6840 (p0) REVERT: A 222 ARG cc_start: 0.5075 (tpt90) cc_final: 0.4067 (tpt-90) REVERT: A 451 MET cc_start: 0.7838 (mmm) cc_final: 0.7531 (mmm) REVERT: A 510 GLN cc_start: 0.5018 (OUTLIER) cc_final: 0.4775 (mt0) REVERT: A 540 LEU cc_start: 0.7614 (tp) cc_final: 0.7287 (tp) REVERT: A 703 ASP cc_start: 0.7029 (p0) cc_final: 0.6709 (p0) REVERT: A 756 GLU cc_start: 0.5582 (OUTLIER) cc_final: 0.5075 (mt-10) REVERT: A 934 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6663 (tp) REVERT: A 1197 HIS cc_start: 0.6529 (OUTLIER) cc_final: 0.6280 (p90) REVERT: B 51 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7878 (mtt-85) REVERT: B 309 VAL cc_start: 0.5979 (OUTLIER) cc_final: 0.5427 (p) outliers start: 43 outliers final: 28 residues processed: 155 average time/residue: 0.3582 time to fit residues: 79.9548 Evaluate side-chains 144 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 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 543 VAL 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 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 59 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 47 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 HIS A1157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.174595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.151930 restraints weight = 49589.762| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.87 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12274 Z= 0.222 Angle : 0.769 11.003 16898 Z= 0.405 Chirality : 0.048 0.206 1905 Planarity : 0.006 0.060 1975 Dihedral : 21.869 171.341 2150 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 3.82 % Allowed : 28.04 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1357 helix: -0.19 (0.23), residues: 459 sheet: -1.27 (0.32), residues: 229 loop : -1.77 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 856 HIS 0.005 0.001 HIS A 192 PHE 0.026 0.003 PHE A 313 TYR 0.022 0.002 TYR A 818 ARG 0.009 0.001 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.04781 ( 489) hydrogen bonds : angle 5.44475 ( 1363) covalent geometry : bond 0.00521 (12274) covalent geometry : angle 0.76887 (16898) *********************** 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 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 1.150 Fit side-chains REVERT: A 155 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6927 (p0) REVERT: A 451 MET cc_start: 0.7895 (mmm) cc_final: 0.7563 (mmm) REVERT: A 510 GLN cc_start: 0.5128 (OUTLIER) cc_final: 0.4812 (mt0) REVERT: A 703 ASP cc_start: 0.7176 (p0) cc_final: 0.6856 (p0) REVERT: A 756 GLU cc_start: 0.5615 (OUTLIER) cc_final: 0.5059 (mt-10) REVERT: A 934 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6757 (tp) REVERT: A 1197 HIS cc_start: 0.6641 (OUTLIER) cc_final: 0.6385 (p90) outliers start: 41 outliers final: 34 residues processed: 143 average time/residue: 0.2799 time to fit residues: 60.3841 Evaluate side-chains 147 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 178 THR 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 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 551 LYS 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 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 59 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 0.0030 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 120 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 768 HIS A 912 HIS A1152 HIS A1157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.181108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.159481 restraints weight = 43501.817| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.12 r_work: 0.3895 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.4276 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= 0.150 Angle : 0.700 9.537 16898 Z= 0.370 Chirality : 0.045 0.194 1905 Planarity : 0.005 0.061 1975 Dihedral : 21.620 172.812 2150 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.69 % Rotamer: Outliers : 3.19 % Allowed : 28.75 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.23), residues: 1357 helix: 0.07 (0.24), residues: 461 sheet: -1.31 (0.32), residues: 228 loop : -1.68 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 856 HIS 0.005 0.001 HIS A 709 PHE 0.021 0.002 PHE A 965 TYR 0.018 0.002 TYR A 818 ARG 0.009 0.001 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 489) hydrogen bonds : angle 5.18105 ( 1363) covalent geometry : bond 0.00339 (12274) covalent geometry : angle 0.69994 (16898) *********************** 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 161 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.179 Fit side-chains REVERT: A 155 ASN cc_start: 0.7245 (OUTLIER) cc_final: 0.6933 (p0) REVERT: A 222 ARG cc_start: 0.5439 (tpt90) cc_final: 0.4238 (tpt-90) REVERT: A 451 MET cc_start: 0.7422 (mmm) cc_final: 0.7080 (mmm) REVERT: A 540 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7561 (tp) REVERT: A 703 ASP cc_start: 0.7234 (p0) cc_final: 0.6841 (p0) REVERT: A 756 GLU cc_start: 0.5511 (OUTLIER) cc_final: 0.5038 (mt-10) REVERT: A 1195 VAL cc_start: 0.7108 (t) cc_final: 0.6577 (m) REVERT: A 1197 HIS cc_start: 0.6879 (OUTLIER) cc_final: 0.6572 (p90) REVERT: B 163 THR cc_start: 0.7620 (p) cc_final: 0.7377 (p) REVERT: B 265 PHE cc_start: 0.5707 (p90) cc_final: 0.5441 (p90) outliers start: 34 outliers final: 24 residues processed: 153 average time/residue: 0.2398 time to fit residues: 54.7083 Evaluate side-chains 139 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 733 PHE 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 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 1197 HIS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 912 HIS A1157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.176128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.155831 restraints weight = 63042.539| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 4.17 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4111 r_free = 0.4111 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4111 r_free = 0.4111 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12274 Z= 0.201 Angle : 0.740 10.294 16898 Z= 0.390 Chirality : 0.047 0.189 1905 Planarity : 0.005 0.062 1975 Dihedral : 21.637 176.103 2150 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.97 % Favored : 92.95 % Rotamer: Outliers : 3.19 % Allowed : 29.02 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.23), residues: 1357 helix: -0.04 (0.24), residues: 457 sheet: -1.20 (0.32), residues: 230 loop : -1.68 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 856 HIS 0.005 0.001 HIS A 192 PHE 0.031 0.002 PHE A 965 TYR 0.027 0.002 TYR A1148 ARG 0.010 0.001 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 489) hydrogen bonds : angle 5.30137 ( 1363) covalent geometry : bond 0.00470 (12274) covalent geometry : angle 0.74004 (16898) ********************** 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 148 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 1.110 Fit side-chains REVERT: A 155 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.6977 (p0) REVERT: A 451 MET cc_start: 0.7880 (mmm) cc_final: 0.7571 (mmm) REVERT: A 703 ASP cc_start: 0.7222 (p0) cc_final: 0.6883 (p0) REVERT: A 756 GLU cc_start: 0.5559 (OUTLIER) cc_final: 0.5027 (mt-10) REVERT: A 1197 HIS cc_start: 0.6656 (OUTLIER) cc_final: 0.6449 (p90) outliers start: 34 outliers final: 29 residues processed: 141 average time/residue: 0.2499 time to fit residues: 51.7543 Evaluate side-chains 142 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 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 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 802 LEU 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 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 66 ILE Chi-restraints excluded: chain B residue 71 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 80 optimal weight: 1.9990 chunk 101 optimal weight: 0.0020 chunk 103 optimal weight: 0.9990 chunk 59 optimal weight: 0.0020 chunk 72 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 825 HIS A 912 HIS A1157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.180243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.158760 restraints weight = 37131.711| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.92 r_work: 0.3915 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12274 Z= 0.147 Angle : 0.694 9.029 16898 Z= 0.366 Chirality : 0.045 0.185 1905 Planarity : 0.005 0.063 1975 Dihedral : 21.485 176.417 2150 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.84 % Allowed : 29.37 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1357 helix: 0.18 (0.24), residues: 460 sheet: -0.98 (0.33), residues: 213 loop : -1.67 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 856 HIS 0.006 0.001 HIS A 709 PHE 0.028 0.002 PHE A 965 TYR 0.024 0.002 TYR A1148 ARG 0.010 0.001 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 489) hydrogen bonds : angle 5.12008 ( 1363) covalent geometry : bond 0.00333 (12274) covalent geometry : angle 0.69433 (16898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5621.44 seconds wall clock time: 101 minutes 35.47 seconds (6095.47 seconds total)