Starting phenix.real_space_refine on Fri Jul 3 07:14:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a6f_11672/07_2026/7a6f_11672.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a6f_11672/07_2026/7a6f_11672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7a6f_11672/07_2026/7a6f_11672.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a6f_11672/07_2026/7a6f_11672.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a6f_11672/07_2026/7a6f_11672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a6f_11672/07_2026/7a6f_11672.map" model { file = "/net/cci-nas-00/data/ceres_data/7a6f_11672/07_2026/7a6f_11672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a6f_11672/07_2026/7a6f_11672.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 8193 2.51 5 N 2092 2.21 5 O 2316 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12655 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 302 Unusual residues: {'CLR': 8, 'ZQU': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 2.70, per 1000 atoms: 0.21 Number of scatterers: 12655 At special positions: 0 Unit cell: (103.32, 208.32, 100.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 F 4 9.00 O 2316 8.00 N 2092 7.00 C 8193 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.05 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.05 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.65 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " distance=2.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 575.1 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 48.5% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 44 through 62 removed outlier: 3.552A pdb=" N VAL A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 80 removed outlier: 3.747A pdb=" N LEU A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 157 removed outlier: 3.560A pdb=" N ALA A 140 " --> pdb=" O TRP A 136 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 187 through 211 removed outlier: 4.316A pdb=" N GLY A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.757A pdb=" N ILE A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 237 Processing helix chain 'A' and resid 246 through 260 removed outlier: 4.263A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 269 through 323 removed outlier: 3.803A pdb=" N GLU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 345 removed outlier: 3.523A pdb=" N VAL A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 371 removed outlier: 4.631A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.822A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 510 through 516 removed outlier: 3.623A pdb=" N MET A 514 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 547 removed outlier: 3.608A pdb=" N ARG A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 575 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.546A pdb=" N THR A 591 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 588 through 592' Processing helix chain 'A' and resid 611 through 619 removed outlier: 3.635A pdb=" N LEU A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 707 through 741 removed outlier: 3.646A pdb=" N PHE A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 4.460A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 797 Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 810 through 852 removed outlier: 3.569A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 862 removed outlier: 3.550A pdb=" N THR A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 880 Processing helix chain 'A' and resid 887 through 903 removed outlier: 3.570A pdb=" N GLY A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 903 " --> pdb=" O GLU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 909 removed outlier: 3.790A pdb=" N SER A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 965 removed outlier: 3.932A pdb=" N MET A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER A 923 " --> pdb=" O MET A 919 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.528A pdb=" N HIS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 939 " --> pdb=" O ALA A 935 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 943 " --> pdb=" O GLY A 939 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 953 " --> pdb=" O MET A 949 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA A 954 " --> pdb=" O TYR A 950 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 993 removed outlier: 3.979A pdb=" N PHE A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1013 Processing helix chain 'A' and resid 1075 through 1084 removed outlier: 3.772A pdb=" N VAL A1079 " --> pdb=" O GLY A1075 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN A1081 " --> pdb=" O SER A1077 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A1082 " --> pdb=" O THR A1078 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1083 " --> pdb=" O VAL A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1113 Processing helix chain 'A' and resid 1126 through 1134 Processing helix chain 'A' and resid 1141 through 1152 removed outlier: 3.619A pdb=" N ILE A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1161 removed outlier: 3.674A pdb=" N SER A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A1161 " --> pdb=" O PHE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1191 removed outlier: 3.929A pdb=" N ARG A1183 " --> pdb=" O GLY A1179 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A1184 " --> pdb=" O GLN A1180 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A1186 " --> pdb=" O GLN A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1220 removed outlier: 3.718A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A1220 " --> pdb=" O GLU A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1262 Processing helix chain 'A' and resid 1265 through 1271 removed outlier: 3.682A pdb=" N SER A1269 " --> pdb=" O GLY A1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 187 through 193 removed outlier: 3.551A pdb=" N ARG B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.812A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.970A pdb=" N ASP C 136 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 414 through 417 removed outlier: 3.828A pdb=" N ARG A 395 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET A 450 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 removed outlier: 4.085A pdb=" N PHE A 399 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 410 " --> pdb=" O PHE A 399 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.904A pdb=" N GLY A 471 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 552 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE A 585 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU A 554 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 423 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR A 422 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA A 599 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA A 424 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE A 601 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A 426 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1053 through 1060 removed outlier: 7.878A pdb=" N GLN A1054 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A1041 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A1056 " --> pdb=" O GLU A1039 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1228 through 1230 removed outlier: 5.703A pdb=" N LEU A1066 " --> pdb=" O VAL A1229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1246 through 1247 removed outlier: 3.567A pdb=" N GLN A1247 " --> pdb=" O ARG A1250 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A1250 " --> pdb=" O GLN A1247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 24 Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'B' and resid 167 through 168 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.162A pdb=" N LEU C 45 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 126 through 130 removed outlier: 3.632A pdb=" N LYS C 149 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 130 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 144 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 160 removed outlier: 3.882A pdb=" N ILE C 199 " --> pdb=" O ILE C 216 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1779 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3945 1.34 - 1.46: 2864 1.46 - 1.58: 6030 1.58 - 1.71: 15 1.71 - 1.83: 83 Bond restraints: 12937 Sorted by residual: bond pdb=" C32 ZQU A1301 " pdb=" N03 ZQU A1301 " ideal model delta sigma weight residual 1.316 1.496 -0.180 2.00e-02 2.50e+03 8.13e+01 bond pdb=" C32 ZQU A1302 " pdb=" N03 ZQU A1302 " ideal model delta sigma weight residual 1.316 1.490 -0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" C17 ZQU A1301 " pdb=" C19 ZQU A1301 " ideal model delta sigma weight residual 1.390 1.561 -0.171 2.00e-02 2.50e+03 7.30e+01 bond pdb=" C17 ZQU A1302 " pdb=" C19 ZQU A1302 " ideal model delta sigma weight residual 1.390 1.561 -0.171 2.00e-02 2.50e+03 7.28e+01 bond pdb=" C07 ZQU A1301 " pdb=" C13 ZQU A1301 " ideal model delta sigma weight residual 1.393 1.557 -0.164 2.00e-02 2.50e+03 6.72e+01 ... (remaining 12932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 17349 3.75 - 7.50: 202 7.50 - 11.25: 16 11.25 - 15.01: 4 15.01 - 18.76: 2 Bond angle restraints: 17573 Sorted by residual: angle pdb=" C03 ZQU A1301 " pdb=" C01 ZQU A1301 " pdb=" C04 ZQU A1301 " ideal model delta sigma weight residual 121.18 139.94 -18.76 3.00e+00 1.11e-01 3.91e+01 angle pdb=" C03 ZQU A1302 " pdb=" C01 ZQU A1302 " pdb=" C04 ZQU A1302 " ideal model delta sigma weight residual 121.18 138.12 -16.94 3.00e+00 1.11e-01 3.19e+01 angle pdb=" C ALA A 883 " pdb=" N LEU A 884 " pdb=" CA LEU A 884 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 angle pdb=" F01 ZQU A1302 " pdb=" C03 ZQU A1302 " pdb=" F02 ZQU A1302 " ideal model delta sigma weight residual 108.18 122.26 -14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" N LYS A1014 " pdb=" CA LYS A1014 " pdb=" C LYS A1014 " ideal model delta sigma weight residual 110.35 116.63 -6.28 1.36e+00 5.41e-01 2.13e+01 ... (remaining 17568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.14: 7218 31.14 - 62.29: 388 62.29 - 93.43: 31 93.43 - 124.58: 3 124.58 - 155.72: 18 Dihedral angle restraints: 7658 sinusoidal: 3072 harmonic: 4586 Sorted by residual: dihedral pdb=" CA ALA C 104 " pdb=" C ALA C 104 " pdb=" N TRP C 105 " pdb=" CA TRP C 105 " ideal model delta harmonic sigma weight residual -180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PHE A1123 " pdb=" C PHE A1123 " pdb=" N ASP A1124 " pdb=" CA ASP A1124 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA TYR A 853 " pdb=" C TYR A 853 " pdb=" N GLY A 854 " pdb=" CA GLY A 854 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 7655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 2028 1.004 - 2.009: 0 2.009 - 3.013: 0 3.013 - 4.017: 0 4.017 - 5.022: 2 Chirality restraints: 2030 Sorted by residual: chirality pdb=" C06 ZQU A1302 " pdb=" C07 ZQU A1302 " pdb=" C08 ZQU A1302 " pdb=" N01 ZQU A1302 " both_signs ideal model delta sigma weight residual False 2.42 -2.60 5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" C06 ZQU A1301 " pdb=" C07 ZQU A1301 " pdb=" C08 ZQU A1301 " pdb=" N01 ZQU A1301 " both_signs ideal model delta sigma weight residual False 2.42 -2.52 4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" C17 CLR A1308 " pdb=" C13 CLR A1308 " pdb=" C16 CLR A1308 " pdb=" C20 CLR A1308 " both_signs ideal model delta sigma weight residual False 2.55 2.99 -0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 2027 not shown) Planarity restraints: 2162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 428 " 0.020 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ASN A 428 " -0.066 2.00e-02 2.50e+03 pdb=" O ASN A 428 " 0.025 2.00e-02 2.50e+03 pdb=" N SER A 429 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1119 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A1120 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A1120 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1120 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 222 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO A 223 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.031 5.00e-02 4.00e+02 ... (remaining 2159 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 14 2.25 - 2.92: 5751 2.92 - 3.58: 17801 3.58 - 4.24: 28244 4.24 - 4.90: 48296 Nonbonded interactions: 100106 Sorted by model distance: nonbonded pdb=" CD1 LEU A 425 " pdb=" CE1 PHE A 601 " model vdw 1.592 3.760 nonbonded pdb=" O SER A1020 " pdb=" CD GLN A1107 " model vdw 2.062 3.270 nonbonded pdb=" CB ALA A 58 " pdb=" OE1 GLN A 132 " model vdw 2.122 3.460 nonbonded pdb=" N ASP A 744 " pdb=" OD1 ASP A 744 " model vdw 2.163 3.120 nonbonded pdb=" O THR A 898 " pdb=" CG2 ILE A 901 " model vdw 2.172 3.460 ... (remaining 100101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.510 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 : 0.014 0.616 12942 Z= 0.694 Angle : 1.136 26.622 17583 Z= 0.646 Chirality : 0.169 5.022 2030 Planarity : 0.005 0.071 2162 Dihedral : 19.963 155.722 4703 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 32.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 1.50 % Allowed : 28.39 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.18), residues: 1584 helix: -2.25 (0.16), residues: 705 sheet: -2.59 (0.30), residues: 264 loop : -3.22 (0.20), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 101 TYR 0.019 0.002 TYR A 310 PHE 0.030 0.002 PHE B 94 TRP 0.021 0.002 TRP A 708 HIS 0.005 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.01248 / 0.64 (12937) covalent geometry : angle 1.10605 / 0.63 (17573) SS BOND : bond 0.27682 / 13.86 ( 5) SS BOND : angle 10.98463 / 4.22 ( 10) hydrogen bonds : bond 0.21691 / 14.62 ( 617) hydrogen bonds : angle 8.58010 / 6.20 ( 1779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.437 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 105 MET cc_start: 0.7287 (ttt) cc_final: 0.6591 (tpp) REVERT: A 276 ARG cc_start: 0.6823 (mtp180) cc_final: 0.6616 (mtp180) REVERT: A 616 MET cc_start: 0.3092 (mtt) cc_final: 0.2578 (mtm) REVERT: A 628 MET cc_start: 0.1775 (tpp) cc_final: 0.1491 (ttt) REVERT: A 1133 TYR cc_start: 0.6890 (t80) cc_final: 0.6647 (t80) REVERT: C 154 GLU cc_start: 0.6801 (tp30) cc_final: 0.6564 (tp30) outliers start: 20 outliers final: 11 residues processed: 144 average time/residue: 0.1099 time to fit residues: 22.4440 Evaluate side-chains 113 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 1014 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 117 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS A 166 HIS A 280 ASN A 347 GLN A 629 GLN A 750 GLN A 809 ASN A 842 ASN A 925 GLN A 990 GLN A1112 HIS A1180 GLN A1193 GLN A1254 HIS A1274 GLN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 212 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 HIS C 202 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.210271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177347 restraints weight = 16868.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.169275 restraints weight = 46798.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.162969 restraints weight = 26588.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.162842 restraints weight = 29924.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.162596 restraints weight = 16573.517| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12942 Z= 0.245 Angle : 0.777 8.518 17583 Z= 0.397 Chirality : 0.047 0.302 2030 Planarity : 0.005 0.052 2162 Dihedral : 17.361 139.224 1895 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.87 % Favored : 94.07 % Rotamer: Outliers : 7.72 % Allowed : 25.24 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.19), residues: 1584 helix: -0.91 (0.18), residues: 717 sheet: -2.09 (0.30), residues: 268 loop : -2.46 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 148 TYR 0.017 0.002 TYR A 116 PHE 0.022 0.002 PHE B 94 TRP 0.019 0.002 TRP A 708 HIS 0.006 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 (12937) covalent geometry : angle 0.77558 / 0.40 (17573) SS BOND : bond 0.00849 / 0.50 ( 5) SS BOND : angle 1.80487 / 1.10 ( 10) hydrogen bonds : bond 0.07677 / 4.91 ( 617) hydrogen bonds : angle 5.71797 / 4.12 ( 1779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 100 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 616 MET cc_start: 0.3090 (mtt) cc_final: 0.2579 (mtm) REVERT: A 702 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6720 (tttt) REVERT: A 876 MET cc_start: 0.8264 (tpt) cc_final: 0.7839 (tpt) REVERT: A 913 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: A 1133 TYR cc_start: 0.6954 (t80) cc_final: 0.6728 (t80) REVERT: C 62 ASP cc_start: 0.7384 (m-30) cc_final: 0.7060 (m-30) outliers start: 103 outliers final: 70 residues processed: 194 average time/residue: 0.1008 time to fit residues: 29.7249 Evaluate side-chains 163 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 91 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1204 SER Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 90 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 125 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 HIS A 946 GLN B 43 GLN C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.214857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.181859 restraints weight = 16933.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.174742 restraints weight = 44444.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.168178 restraints weight = 24774.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.168117 restraints weight = 27671.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.167600 restraints weight = 16312.539| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12942 Z= 0.144 Angle : 0.644 8.596 17583 Z= 0.328 Chirality : 0.043 0.298 2030 Planarity : 0.004 0.049 2162 Dihedral : 17.070 137.265 1879 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.89 % Allowed : 25.84 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.20), residues: 1584 helix: 0.04 (0.19), residues: 739 sheet: -1.62 (0.32), residues: 245 loop : -2.09 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 489 TYR 0.013 0.001 TYR C 100 PHE 0.014 0.001 PHE A 512 TRP 0.016 0.001 TRP A 708 HIS 0.006 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (12937) covalent geometry : angle 0.64195 / 0.33 (17573) SS BOND : bond 0.00867 / 0.47 ( 5) SS BOND : angle 2.21881 / 1.33 ( 10) hydrogen bonds : bond 0.06059 / 3.83 ( 617) hydrogen bonds : angle 5.00470 / 3.61 ( 1779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 95 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 111 MET cc_start: 0.6400 (mmm) cc_final: 0.6023 (mmm) REVERT: A 876 MET cc_start: 0.8161 (tpt) cc_final: 0.7812 (tpt) REVERT: C 62 ASP cc_start: 0.7393 (m-30) cc_final: 0.6941 (m-30) outliers start: 92 outliers final: 65 residues processed: 177 average time/residue: 0.1058 time to fit residues: 28.1007 Evaluate side-chains 152 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 87 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 946 GLN Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1204 SER Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 192 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 61 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 143 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 ASN A1064 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.215022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.183650 restraints weight = 16881.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.176685 restraints weight = 41967.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.171995 restraints weight = 24500.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171342 restraints weight = 27524.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.171066 restraints weight = 17072.236| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12942 Z= 0.146 Angle : 0.627 9.727 17583 Z= 0.316 Chirality : 0.043 0.266 2030 Planarity : 0.004 0.042 2162 Dihedral : 16.955 137.505 1877 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 6.44 % Allowed : 26.97 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.21), residues: 1584 helix: 0.32 (0.19), residues: 740 sheet: -1.38 (0.32), residues: 245 loop : -1.86 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.018 0.001 TYR A1133 PHE 0.016 0.001 PHE A 942 TRP 0.013 0.001 TRP A 708 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (12937) covalent geometry : angle 0.62514 / 0.32 (17573) SS BOND : bond 0.00788 / 0.45 ( 5) SS BOND : angle 1.86614 / 1.15 ( 10) hydrogen bonds : bond 0.05845 / 3.70 ( 617) hydrogen bonds : angle 4.80077 / 3.46 ( 1779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 90 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 111 MET cc_start: 0.6423 (mmm) cc_final: 0.5992 (mmm) REVERT: A 616 MET cc_start: 0.2874 (mtt) cc_final: 0.2623 (mtm) REVERT: A 876 MET cc_start: 0.8203 (tpt) cc_final: 0.7859 (tpt) REVERT: B 190 GLU cc_start: 0.4843 (mp0) cc_final: 0.4224 (tt0) REVERT: C 62 ASP cc_start: 0.7415 (m-30) cc_final: 0.6955 (m-30) outliers start: 86 outliers final: 67 residues processed: 166 average time/residue: 0.1009 time to fit residues: 25.6795 Evaluate side-chains 154 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 87 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 192 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 112 optimal weight: 30.0000 chunk 15 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.215104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.181590 restraints weight = 16853.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.175569 restraints weight = 44882.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.171189 restraints weight = 25579.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.170643 restraints weight = 27955.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.170463 restraints weight = 17054.471| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12942 Z= 0.147 Angle : 0.612 8.339 17583 Z= 0.310 Chirality : 0.043 0.272 2030 Planarity : 0.003 0.040 2162 Dihedral : 16.878 137.458 1877 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 7.42 % Allowed : 25.54 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.21), residues: 1584 helix: 0.51 (0.19), residues: 734 sheet: -1.36 (0.30), residues: 259 loop : -1.77 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1147 TYR 0.022 0.001 TYR A1133 PHE 0.015 0.001 PHE A 512 TRP 0.012 0.001 TRP A 708 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (12937) covalent geometry : angle 0.61101 / 0.31 (17573) SS BOND : bond 0.00760 / 0.44 ( 5) SS BOND : angle 1.71998 / 1.08 ( 10) hydrogen bonds : bond 0.05709 / 3.60 ( 617) hydrogen bonds : angle 4.67506 / 3.37 ( 1779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 94 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 111 MET cc_start: 0.6256 (mmm) cc_final: 0.5934 (mmm) REVERT: A 876 MET cc_start: 0.8141 (tpt) cc_final: 0.7775 (tpt) REVERT: C 33 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8749 (m) REVERT: C 62 ASP cc_start: 0.7396 (m-30) cc_final: 0.6917 (m-30) outliers start: 99 outliers final: 74 residues processed: 180 average time/residue: 0.0962 time to fit residues: 26.3100 Evaluate side-chains 166 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 91 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 192 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.0370 chunk 137 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 43 optimal weight: 0.0870 chunk 35 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.217696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.186229 restraints weight = 16806.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.179074 restraints weight = 40164.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.172878 restraints weight = 24994.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.172850 restraints weight = 27747.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.172204 restraints weight = 18216.588| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12942 Z= 0.119 Angle : 0.578 8.232 17583 Z= 0.292 Chirality : 0.042 0.264 2030 Planarity : 0.003 0.039 2162 Dihedral : 16.787 137.178 1877 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.32 % Allowed : 27.27 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.21), residues: 1584 helix: 0.91 (0.20), residues: 724 sheet: -1.23 (0.31), residues: 251 loop : -1.54 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.019 0.001 TYR A1133 PHE 0.015 0.001 PHE A 512 TRP 0.012 0.001 TRP A 708 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (12937) covalent geometry : angle 0.57672 / 0.29 (17573) SS BOND : bond 0.00604 / 0.35 ( 5) SS BOND : angle 1.73593 / 1.11 ( 10) hydrogen bonds : bond 0.05091 / 3.21 ( 617) hydrogen bonds : angle 4.45953 / 3.21 ( 1779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 101 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 733 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8828 (m) REVERT: A 876 MET cc_start: 0.8107 (tpt) cc_final: 0.7795 (tpt) REVERT: A 1021 TYR cc_start: 0.4173 (OUTLIER) cc_final: 0.2047 (t80) REVERT: B 190 GLU cc_start: 0.4571 (mp0) cc_final: 0.4231 (mt-10) REVERT: C 62 ASP cc_start: 0.7427 (m-30) cc_final: 0.6980 (m-30) outliers start: 71 outliers final: 55 residues processed: 164 average time/residue: 0.0963 time to fit residues: 23.8786 Evaluate side-chains 149 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 92 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1021 TYR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 192 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.213742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.182196 restraints weight = 16840.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.175751 restraints weight = 43375.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.170892 restraints weight = 24815.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170200 restraints weight = 29142.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.169585 restraints weight = 18120.590| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12942 Z= 0.189 Angle : 0.652 8.035 17583 Z= 0.328 Chirality : 0.044 0.281 2030 Planarity : 0.004 0.040 2162 Dihedral : 16.838 137.630 1877 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 6.14 % Allowed : 27.19 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1584 helix: 0.65 (0.19), residues: 727 sheet: -1.16 (0.31), residues: 251 loop : -1.54 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.025 0.002 TYR A1133 PHE 0.017 0.002 PHE B 94 TRP 0.009 0.001 TRP A 708 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (12937) covalent geometry : angle 0.64999 / 0.33 (17573) SS BOND : bond 0.00877 / 0.53 ( 5) SS BOND : angle 2.08548 / 1.32 ( 10) hydrogen bonds : bond 0.05916 / 3.73 ( 617) hydrogen bonds : angle 4.62570 / 3.32 ( 1779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 96 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 876 MET cc_start: 0.8198 (tpt) cc_final: 0.7838 (tpt) REVERT: A 1021 TYR cc_start: 0.4230 (OUTLIER) cc_final: 0.2028 (t80) REVERT: B 190 GLU cc_start: 0.4477 (mp0) cc_final: 0.4151 (mt-10) outliers start: 82 outliers final: 71 residues processed: 171 average time/residue: 0.0915 time to fit residues: 23.6595 Evaluate side-chains 163 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 91 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1021 TYR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 187 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 126 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 112 optimal weight: 40.0000 chunk 115 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 GLN A 508 ASN A 570 GLN ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.216402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.180292 restraints weight = 16729.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.179029 restraints weight = 43341.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.173109 restraints weight = 21279.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.172323 restraints weight = 25583.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.172258 restraints weight = 14112.553| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12942 Z= 0.131 Angle : 0.599 8.267 17583 Z= 0.300 Chirality : 0.042 0.266 2030 Planarity : 0.003 0.041 2162 Dihedral : 16.760 137.317 1877 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.47 % Allowed : 28.01 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.21), residues: 1584 helix: 0.88 (0.19), residues: 735 sheet: -1.03 (0.32), residues: 249 loop : -1.49 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.021 0.001 TYR A1133 PHE 0.017 0.001 PHE C 172 TRP 0.026 0.001 TRP C 160 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (12937) covalent geometry : angle 0.59790 / 0.30 (17573) SS BOND : bond 0.00713 / 0.43 ( 5) SS BOND : angle 1.72440 / 1.07 ( 10) hydrogen bonds : bond 0.05300 / 3.33 ( 617) hydrogen bonds : angle 4.46793 / 3.20 ( 1779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 94 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 184 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7351 (mt-10) REVERT: A 876 MET cc_start: 0.8153 (tpt) cc_final: 0.7845 (tpt) REVERT: A 1021 TYR cc_start: 0.4367 (OUTLIER) cc_final: 0.2090 (t80) REVERT: A 1151 GLU cc_start: 0.5311 (OUTLIER) cc_final: 0.4864 (tt0) REVERT: B 190 GLU cc_start: 0.4452 (mp0) cc_final: 0.4156 (mt-10) outliers start: 73 outliers final: 64 residues processed: 161 average time/residue: 0.1020 time to fit residues: 24.7656 Evaluate side-chains 158 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 92 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1021 TYR Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 155 optimal weight: 0.2980 chunk 74 optimal weight: 0.4980 chunk 139 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 47 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 30.0000 chunk 156 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.218086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.187042 restraints weight = 16780.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.179820 restraints weight = 41745.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.174262 restraints weight = 25886.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.174011 restraints weight = 28782.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.173682 restraints weight = 16648.663| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12942 Z= 0.117 Angle : 0.587 9.648 17583 Z= 0.292 Chirality : 0.042 0.266 2030 Planarity : 0.003 0.040 2162 Dihedral : 16.700 137.150 1877 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.94 % Allowed : 28.76 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.21), residues: 1584 helix: 1.08 (0.19), residues: 736 sheet: -0.76 (0.32), residues: 258 loop : -1.47 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 442 TYR 0.018 0.001 TYR A1133 PHE 0.017 0.001 PHE A 512 TRP 0.023 0.001 TRP C 160 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (12937) covalent geometry : angle 0.58590 / 0.29 (17573) SS BOND : bond 0.00604 / 0.36 ( 5) SS BOND : angle 1.50838 / 0.95 ( 10) hydrogen bonds : bond 0.04926 / 3.09 ( 617) hydrogen bonds : angle 4.34481 / 3.11 ( 1779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 98 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 733 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8865 (m) REVERT: A 876 MET cc_start: 0.8134 (tpt) cc_final: 0.7842 (tpt) REVERT: A 1021 TYR cc_start: 0.4365 (OUTLIER) cc_final: 0.2157 (t80) REVERT: A 1151 GLU cc_start: 0.5306 (OUTLIER) cc_final: 0.4875 (tt0) REVERT: B 190 GLU cc_start: 0.4402 (mp0) cc_final: 0.4127 (mt-10) outliers start: 66 outliers final: 57 residues processed: 158 average time/residue: 0.0925 time to fit residues: 22.1546 Evaluate side-chains 154 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 94 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1021 TYR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 155 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 ASN ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.215440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.186433 restraints weight = 16876.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.177503 restraints weight = 41689.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.171980 restraints weight = 29698.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.171659 restraints weight = 29665.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.170929 restraints weight = 18337.083| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12942 Z= 0.194 Angle : 0.662 9.462 17583 Z= 0.332 Chirality : 0.044 0.279 2030 Planarity : 0.004 0.039 2162 Dihedral : 16.794 137.731 1877 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.94 % Allowed : 28.54 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1584 helix: 0.73 (0.19), residues: 733 sheet: -0.82 (0.32), residues: 258 loop : -1.54 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 113 TYR 0.023 0.002 TYR A1133 PHE 0.017 0.002 PHE B 94 TRP 0.021 0.002 TRP C 160 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (12937) covalent geometry : angle 0.66014 / 0.33 (17573) SS BOND : bond 0.00887 / 0.54 ( 5) SS BOND : angle 1.94402 / 1.22 ( 10) hydrogen bonds : bond 0.05980 / 3.75 ( 617) hydrogen bonds : angle 4.59080 / 3.28 ( 1779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 90 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 876 MET cc_start: 0.8203 (tpt) cc_final: 0.7863 (tpt) REVERT: A 1021 TYR cc_start: 0.4391 (OUTLIER) cc_final: 0.2031 (t80) REVERT: A 1151 GLU cc_start: 0.5393 (OUTLIER) cc_final: 0.4915 (tt0) REVERT: B 190 GLU cc_start: 0.4628 (mp0) cc_final: 0.4347 (mt-10) outliers start: 66 outliers final: 59 residues processed: 150 average time/residue: 0.1022 time to fit residues: 23.0068 Evaluate side-chains 150 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 89 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1021 TYR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 115 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 ASN ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.218039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.189335 restraints weight = 16722.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.180568 restraints weight = 41622.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.175315 restraints weight = 30497.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.175039 restraints weight = 30900.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174650 restraints weight = 17601.869| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12942 Z= 0.137 Angle : 0.610 9.084 17583 Z= 0.304 Chirality : 0.043 0.268 2030 Planarity : 0.003 0.040 2162 Dihedral : 16.717 137.353 1877 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.94 % Allowed : 28.39 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.21), residues: 1584 helix: 0.94 (0.19), residues: 732 sheet: -0.69 (0.33), residues: 249 loop : -1.51 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 538 TYR 0.021 0.001 TYR A1133 PHE 0.015 0.001 PHE A 512 TRP 0.022 0.001 TRP C 160 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (12937) covalent geometry : angle 0.60917 / 0.30 (17573) SS BOND : bond 0.00725 / 0.43 ( 5) SS BOND : angle 1.62671 / 1.01 ( 10) hydrogen bonds : bond 0.05369 / 3.36 ( 617) hydrogen bonds : angle 4.45324 / 3.18 ( 1779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1948.92 seconds wall clock time: 34 minutes 41.31 seconds (2081.31 seconds total)