Starting phenix.real_space_refine on Wed Jul 30 21:48:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a6f_11672/07_2025/7a6f_11672.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a6f_11672/07_2025/7a6f_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7a6f_11672/07_2025/7a6f_11672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a6f_11672/07_2025/7a6f_11672.map" model { file = "/net/cci-nas-00/data/ceres_data/7a6f_11672/07_2025/7a6f_11672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a6f_11672/07_2025/7a6f_11672.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.40, per 1000 atoms: 0.74 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: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.60 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: 5.59 Time building geometry restraints manager: 4.06 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: 7652 31.14 - 62.29: 402 62.29 - 93.43: 31 93.43 - 124.58: 3 124.58 - 155.72: 18 Dihedral angle restraints: 8106 sinusoidal: 3520 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 8103 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: 0.010 Normalize map: mean=0, sd=1: 91.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.570 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 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 : 19.432 155.722 5151 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 33.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (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 TRP 0.021 0.002 TRP A 708 HIS 0.005 0.001 HIS A 166 PHE 0.030 0.002 PHE B 94 TYR 0.019 0.002 TYR A 310 ARG 0.007 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.21691 ( 617) hydrogen bonds : angle 8.58010 ( 1779) SS BOND : bond 0.27682 ( 5) SS BOND : angle 10.98463 ( 10) covalent geometry : bond 0.01248 (12937) covalent geometry : angle 1.10605 (17573) *********************** 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 : 1.260 Fit side-chains revert: symmetry clash 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: 0.6590 (tpp) REVERT: A 276 ARG cc_start: 0.6823 (mtp180) cc_final: 0.6617 (mtp180) REVERT: A 616 MET cc_start: 0.3092 (mtt) cc_final: 0.2580 (mtm) REVERT: A 628 MET cc_start: 0.1775 (tpp) cc_final: 0.1492 (ttt) REVERT: A 1133 TYR cc_start: 0.6890 (t80) cc_final: 0.6648 (t80) REVERT: C 154 GLU cc_start: 0.6801 (tp30) cc_final: 0.6565 (tp30) outliers start: 20 outliers final: 11 residues processed: 144 average time/residue: 0.2876 time to fit residues: 58.5241 Evaluate side-chains 114 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 133 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 30.0000 chunk 143 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 280 ASN A 347 GLN A 629 GLN A 750 GLN A 809 ASN A 842 ASN A 990 GLN A1112 HIS A1180 GLN A1254 HIS A1274 GLN B 43 GLN B 212 ASN C 39 GLN C 170 HIS C 202 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.215469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.183223 restraints weight = 16700.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.177169 restraints weight = 43166.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.172404 restraints weight = 25105.618| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12942 Z= 0.153 Angle : 0.694 8.809 17583 Z= 0.353 Chirality : 0.044 0.219 2030 Planarity : 0.004 0.050 2162 Dihedral : 16.007 138.857 2343 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.45 % Rotamer: Outliers : 5.92 % Allowed : 24.49 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.20), residues: 1584 helix: -0.44 (0.18), residues: 723 sheet: -1.86 (0.32), residues: 245 loop : -2.37 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 708 HIS 0.006 0.001 HIS C 205 PHE 0.014 0.001 PHE A 204 TYR 0.018 0.002 TYR A 920 ARG 0.005 0.001 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.06578 ( 617) hydrogen bonds : angle 5.35522 ( 1779) SS BOND : bond 0.00680 ( 5) SS BOND : angle 1.37311 ( 10) covalent geometry : bond 0.00312 (12937) covalent geometry : angle 0.69306 (17573) *********************** 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 188 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 109 time to evaluate : 1.388 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 51 MET cc_start: 0.7907 (mtt) cc_final: 0.7642 (mtp) REVERT: A 616 MET cc_start: 0.3243 (mtt) cc_final: 0.2736 (mtm) REVERT: A 733 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.8921 (m) REVERT: A 1133 TYR cc_start: 0.6950 (t80) cc_final: 0.6709 (t80) REVERT: B 193 ARG cc_start: 0.6386 (ttm170) cc_final: 0.5363 (ttp-170) REVERT: C 62 ASP cc_start: 0.7441 (m-30) cc_final: 0.7128 (m-30) outliers start: 79 outliers final: 46 residues processed: 179 average time/residue: 0.2268 time to fit residues: 60.8242 Evaluate side-chains 142 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 95 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 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 345 VAL Chi-restraints excluded: chain A residue 368 ILE 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 733 SER Chi-restraints excluded: chain A residue 752 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 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 970 SER Chi-restraints excluded: chain A residue 993 SER 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 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 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 214 CYS 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 142 VAL 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 95 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 120 optimal weight: 0.2980 chunk 129 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 GLN A1193 GLN B 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.209002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.174421 restraints weight = 16982.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.168345 restraints weight = 49109.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.163807 restraints weight = 24319.936| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 12942 Z= 0.308 Angle : 0.790 8.522 17583 Z= 0.403 Chirality : 0.049 0.318 2030 Planarity : 0.005 0.051 2162 Dihedral : 16.048 137.916 2327 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 7.94 % Allowed : 24.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.20), residues: 1584 helix: -0.46 (0.18), residues: 729 sheet: -1.82 (0.30), residues: 266 loop : -2.14 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 708 HIS 0.004 0.001 HIS B 31 PHE 0.027 0.002 PHE B 94 TYR 0.020 0.002 TYR B 54 ARG 0.004 0.001 ARG A 787 Details of bonding type rmsd hydrogen bonds : bond 0.07614 ( 617) hydrogen bonds : angle 5.49302 ( 1779) SS BOND : bond 0.01064 ( 5) SS BOND : angle 3.00712 ( 10) covalent geometry : bond 0.00734 (12937) covalent geometry : angle 0.78695 (17573) *********************** 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 202 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 96 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 171 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.6027 (mp) REVERT: A 616 MET cc_start: 0.3276 (mtt) cc_final: 0.2894 (mtm) REVERT: A 701 MET cc_start: 0.7871 (tpt) cc_final: 0.7666 (tpt) REVERT: A 876 MET cc_start: 0.8157 (tpt) cc_final: 0.7804 (tpt) REVERT: B 190 GLU cc_start: 0.4908 (mp0) cc_final: 0.4089 (tt0) REVERT: C 62 ASP cc_start: 0.7436 (m-30) cc_final: 0.6954 (m-30) REVERT: C 83 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7855 (ptm) outliers start: 106 outliers final: 82 residues processed: 190 average time/residue: 0.2265 time to fit residues: 65.1884 Evaluate side-chains 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 93 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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 165 VAL Chi-restraints excluded: chain A residue 171 LEU 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 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 453 VAL Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 697 PHE 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 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 898 THR 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 946 GLN Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 972 GLU 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 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 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 109 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 4 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 83 MET 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 170 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER 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 38 optimal weight: 30.0000 chunk 59 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN A 946 GLN A1034 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.215008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.182626 restraints weight = 16802.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.174530 restraints weight = 42367.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169761 restraints weight = 24906.896| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12942 Z= 0.141 Angle : 0.627 9.002 17583 Z= 0.319 Chirality : 0.043 0.266 2030 Planarity : 0.004 0.044 2162 Dihedral : 15.747 137.501 2327 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.82 % Allowed : 26.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1584 helix: 0.18 (0.19), residues: 740 sheet: -1.43 (0.31), residues: 255 loop : -1.90 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 708 HIS 0.006 0.001 HIS C 205 PHE 0.015 0.001 PHE A 512 TYR 0.017 0.001 TYR A1133 ARG 0.006 0.000 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.06005 ( 617) hydrogen bonds : angle 4.92626 ( 1779) SS BOND : bond 0.00792 ( 5) SS BOND : angle 1.94857 ( 10) covalent geometry : bond 0.00304 (12937) covalent geometry : angle 0.62595 (17573) *********************** 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 186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 95 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 171 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5910 (mp) REVERT: A 441 GLN cc_start: 0.3144 (OUTLIER) cc_final: 0.2904 (tt0) REVERT: A 701 MET cc_start: 0.7877 (tpt) cc_final: 0.7668 (tpt) REVERT: A 733 SER cc_start: 0.9198 (OUTLIER) cc_final: 0.8903 (m) REVERT: A 876 MET cc_start: 0.8121 (tpt) cc_final: 0.7813 (tpt) REVERT: B 190 GLU cc_start: 0.4883 (mp0) cc_final: 0.4094 (tt0) REVERT: C 62 ASP cc_start: 0.7451 (m-30) cc_final: 0.6987 (m-30) outliers start: 91 outliers final: 62 residues processed: 177 average time/residue: 0.2272 time to fit residues: 60.5734 Evaluate side-chains 155 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 90 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 337 SER 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 441 GLN Chi-restraints excluded: chain A residue 454 ASP 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 719 ILE 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 993 SER 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 1204 SER 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 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 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 133 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 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 75 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.214628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.180807 restraints weight = 16876.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.175261 restraints weight = 44541.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.170874 restraints weight = 24053.201| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12942 Z= 0.153 Angle : 0.628 8.713 17583 Z= 0.318 Chirality : 0.043 0.267 2030 Planarity : 0.003 0.041 2162 Dihedral : 15.636 137.506 2325 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.67 % Allowed : 27.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1584 helix: 0.35 (0.19), residues: 734 sheet: -1.26 (0.31), residues: 259 loop : -1.84 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 708 HIS 0.005 0.001 HIS C 205 PHE 0.016 0.001 PHE A 942 TYR 0.025 0.001 TYR A1133 ARG 0.002 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.05920 ( 617) hydrogen bonds : angle 4.80086 ( 1779) SS BOND : bond 0.00787 ( 5) SS BOND : angle 1.71425 ( 10) covalent geometry : bond 0.00346 (12937) covalent geometry : angle 0.62636 (17573) *********************** 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 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 94 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 171 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5911 (mp) REVERT: A 441 GLN cc_start: 0.3101 (OUTLIER) cc_final: 0.2866 (tt0) REVERT: A 876 MET cc_start: 0.8205 (tpt) cc_final: 0.7992 (tpt) REVERT: B 190 GLU cc_start: 0.4908 (mp0) cc_final: 0.4276 (tt0) REVERT: C 62 ASP cc_start: 0.7467 (m-30) cc_final: 0.6997 (m-30) outliers start: 89 outliers final: 67 residues processed: 175 average time/residue: 0.2315 time to fit residues: 60.0756 Evaluate side-chains 161 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 92 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 156 MET Chi-restraints excluded: chain A residue 171 LEU 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 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 441 GLN 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 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 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 986 MET 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 121 SER Chi-restraints excluded: chain B residue 139 CYS 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 181 SER 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 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 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 86 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4515 r_free = 0.4515 target = 0.214855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.182716 restraints weight = 16926.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.176016 restraints weight = 43587.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170677 restraints weight = 23697.607| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12942 Z= 0.147 Angle : 0.617 9.006 17583 Z= 0.312 Chirality : 0.043 0.267 2030 Planarity : 0.003 0.040 2162 Dihedral : 15.567 137.466 2325 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 6.37 % Allowed : 26.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.21), residues: 1584 helix: 0.48 (0.19), residues: 734 sheet: -1.27 (0.30), residues: 269 loop : -1.72 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 708 HIS 0.005 0.001 HIS C 205 PHE 0.015 0.001 PHE B 94 TYR 0.025 0.001 TYR A1133 ARG 0.008 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.05722 ( 617) hydrogen bonds : angle 4.69740 ( 1779) SS BOND : bond 0.00757 ( 5) SS BOND : angle 1.59129 ( 10) covalent geometry : bond 0.00330 (12937) covalent geometry : angle 0.61642 (17573) *********************** 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 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 100 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 441 GLN cc_start: 0.3110 (OUTLIER) cc_final: 0.2857 (tt0) REVERT: A 733 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8837 (m) REVERT: A 1021 TYR cc_start: 0.4209 (OUTLIER) cc_final: 0.2004 (t80) REVERT: B 190 GLU cc_start: 0.4870 (mp0) cc_final: 0.4273 (tt0) REVERT: C 62 ASP cc_start: 0.7435 (m-30) cc_final: 0.6961 (m-30) outliers start: 85 outliers final: 70 residues processed: 174 average time/residue: 0.2288 time to fit residues: 59.4576 Evaluate side-chains 164 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 91 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 156 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 337 SER 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 441 GLN 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 719 ILE 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 904 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 923 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 1021 TYR 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 101 ARG Chi-restraints excluded: chain B residue 111 ILE 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 181 SER 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 127 VAL Chi-restraints excluded: chain C residue 133 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 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 117 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 30.0000 chunk 129 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.215920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.178954 restraints weight = 16814.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.177899 restraints weight = 44602.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.172066 restraints weight = 20254.366| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12942 Z= 0.136 Angle : 0.606 8.381 17583 Z= 0.306 Chirality : 0.043 0.266 2030 Planarity : 0.003 0.039 2162 Dihedral : 15.494 137.346 2325 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 6.07 % Allowed : 27.79 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1584 helix: 0.67 (0.19), residues: 732 sheet: -1.14 (0.31), residues: 261 loop : -1.60 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 708 HIS 0.005 0.001 HIS C 205 PHE 0.015 0.001 PHE B 94 TYR 0.023 0.001 TYR A1133 ARG 0.003 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.05463 ( 617) hydrogen bonds : angle 4.59682 ( 1779) SS BOND : bond 0.00733 ( 5) SS BOND : angle 1.82880 ( 10) covalent geometry : bond 0.00300 (12937) covalent geometry : angle 0.60462 (17573) *********************** 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 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 101 time to evaluate : 1.241 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 733 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8918 (m) REVERT: A 1021 TYR cc_start: 0.4245 (OUTLIER) cc_final: 0.2038 (t80) REVERT: A 1151 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4838 (tt0) REVERT: B 190 GLU cc_start: 0.4692 (mp0) cc_final: 0.4156 (tt0) REVERT: C 62 ASP cc_start: 0.7363 (m-30) cc_final: 0.6901 (m-30) outliers start: 81 outliers final: 64 residues processed: 172 average time/residue: 0.2215 time to fit residues: 57.5577 Evaluate side-chains 161 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 94 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 156 MET 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 719 ILE 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 865 VAL Chi-restraints excluded: chain A residue 904 PHE 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 1213 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 VAL 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 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 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 20 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.214796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.182244 restraints weight = 16907.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.175926 restraints weight = 44347.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171188 restraints weight = 23783.394| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12942 Z= 0.162 Angle : 0.632 9.911 17583 Z= 0.318 Chirality : 0.044 0.271 2030 Planarity : 0.003 0.038 2162 Dihedral : 15.520 137.499 2325 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.14 % Allowed : 28.01 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1584 helix: 0.69 (0.19), residues: 727 sheet: -1.11 (0.31), residues: 261 loop : -1.53 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 160 HIS 0.005 0.001 HIS C 205 PHE 0.016 0.001 PHE B 94 TYR 0.026 0.001 TYR A1133 ARG 0.006 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.05677 ( 617) hydrogen bonds : angle 4.61010 ( 1779) SS BOND : bond 0.00808 ( 5) SS BOND : angle 1.86127 ( 10) covalent geometry : bond 0.00373 (12937) covalent geometry : angle 0.63079 (17573) *********************** 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 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 98 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 1021 TYR cc_start: 0.4267 (OUTLIER) cc_final: 0.1984 (t80) REVERT: A 1151 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4836 (tt0) REVERT: B 190 GLU cc_start: 0.4602 (mp0) cc_final: 0.4337 (mt-10) REVERT: C 33 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8761 (m) outliers start: 82 outliers final: 72 residues processed: 169 average time/residue: 0.2370 time to fit residues: 60.1074 Evaluate side-chains 168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 93 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 156 MET Chi-restraints excluded: chain A residue 283 GLU 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 440 MET 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 904 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 923 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 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 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 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 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 96 CYS 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 142 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 chunk 78 optimal weight: 0.3980 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 30.0000 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.216456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.184907 restraints weight = 16900.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.178306 restraints weight = 41247.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.173308 restraints weight = 22391.538| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3196 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= 0.134 Angle : 0.606 8.418 17583 Z= 0.305 Chirality : 0.043 0.265 2030 Planarity : 0.003 0.039 2162 Dihedral : 15.445 137.330 2325 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.24 % Allowed : 29.21 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1584 helix: 0.89 (0.19), residues: 728 sheet: -0.97 (0.31), residues: 261 loop : -1.48 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 160 HIS 0.005 0.001 HIS C 205 PHE 0.016 0.001 PHE A 512 TYR 0.024 0.001 TYR A1133 ARG 0.006 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.05320 ( 617) hydrogen bonds : angle 4.47972 ( 1779) SS BOND : bond 0.00717 ( 5) SS BOND : angle 1.62195 ( 10) covalent geometry : bond 0.00297 (12937) covalent geometry : angle 0.60463 (17573) *********************** 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: 70 poor density : 94 time to evaluate : 1.256 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: 0.9183 (OUTLIER) cc_final: 0.8902 (m) REVERT: A 1021 TYR cc_start: 0.4279 (OUTLIER) cc_final: 0.2033 (t80) REVERT: A 1151 GLU cc_start: 0.5329 (OUTLIER) cc_final: 0.4864 (tt0) REVERT: B 190 GLU cc_start: 0.4468 (mp0) cc_final: 0.4179 (mt-10) outliers start: 70 outliers final: 61 residues processed: 155 average time/residue: 0.2562 time to fit residues: 58.8746 Evaluate side-chains 155 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 91 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 440 MET Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 495 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 904 PHE 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 1213 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 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 122 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 74 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.216271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.184645 restraints weight = 16823.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.176661 restraints weight = 41093.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.171264 restraints weight = 24644.557| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12942 Z= 0.141 Angle : 0.613 8.166 17583 Z= 0.309 Chirality : 0.043 0.267 2030 Planarity : 0.003 0.040 2162 Dihedral : 15.438 137.411 2325 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.32 % Allowed : 28.99 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1584 helix: 0.89 (0.19), residues: 734 sheet: -0.88 (0.32), residues: 258 loop : -1.49 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 160 HIS 0.005 0.001 HIS C 205 PHE 0.015 0.001 PHE B 94 TYR 0.022 0.001 TYR A1133 ARG 0.006 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.05373 ( 617) hydrogen bonds : angle 4.45916 ( 1779) SS BOND : bond 0.00730 ( 5) SS BOND : angle 1.70823 ( 10) covalent geometry : bond 0.00319 (12937) covalent geometry : angle 0.61208 (17573) ********************** 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 166 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 95 time to evaluate : 1.304 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: 0.9206 (OUTLIER) cc_final: 0.8921 (m) REVERT: A 1021 TYR cc_start: 0.4396 (OUTLIER) cc_final: 0.2191 (t80) REVERT: A 1151 GLU cc_start: 0.5349 (OUTLIER) cc_final: 0.4909 (tt0) REVERT: B 190 GLU cc_start: 0.4591 (mp0) cc_final: 0.4330 (mt-10) outliers start: 71 outliers final: 62 residues processed: 158 average time/residue: 0.2543 time to fit residues: 60.2908 Evaluate side-chains 159 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 94 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 283 GLU 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 440 MET Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 495 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 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 904 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 923 SER 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 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 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 9 VAL 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 133 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 52 optimal weight: 0.0170 chunk 157 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 108 optimal weight: 0.0670 chunk 99 optimal weight: 7.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.220538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.182786 restraints weight = 16609.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.182871 restraints weight = 43065.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.177674 restraints weight = 21420.473| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3481 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= 0.118 Angle : 0.587 8.035 17583 Z= 0.295 Chirality : 0.042 0.264 2030 Planarity : 0.003 0.040 2162 Dihedral : 15.348 137.150 2325 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.09 % Allowed : 29.14 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1584 helix: 1.07 (0.19), residues: 729 sheet: -0.70 (0.33), residues: 249 loop : -1.39 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 160 HIS 0.005 0.001 HIS C 205 PHE 0.014 0.001 PHE A 512 TYR 0.019 0.001 TYR A1133 ARG 0.004 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.04918 ( 617) hydrogen bonds : angle 4.35498 ( 1779) SS BOND : bond 0.00617 ( 5) SS BOND : angle 1.50093 ( 10) covalent geometry : bond 0.00252 (12937) covalent geometry : angle 0.58619 (17573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5594.47 seconds wall clock time: 100 minutes 33.86 seconds (6033.86 seconds total)