Starting phenix.real_space_refine on Fri Feb 14 12:42:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8buz_16252/02_2025/8buz_16252_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8buz_16252/02_2025/8buz_16252.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/8buz_16252/02_2025/8buz_16252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8buz_16252/02_2025/8buz_16252.map" model { file = "/net/cci-nas-00/data/ceres_data/8buz_16252/02_2025/8buz_16252_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8buz_16252/02_2025/8buz_16252_neut.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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 6344 2.51 5 N 1702 2.21 5 O 1810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9921 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7120 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 19, 'TRANS': 870} Chain breaks: 3 Chain: "B" Number of atoms: 2739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2739 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 13, 'TRANS': 319} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'FOK': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.04, per 1000 atoms: 0.51 Number of scatterers: 9921 At special positions: 0 Unit cell: (151.8, 115.5, 129.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 61 16.00 P 3 15.00 Mg 1 11.99 O 1810 8.00 N 1702 7.00 C 6344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 469 " distance=2.04 Simple disulfide: pdb=" SG CYS A 809 " - pdb=" SG CYS A 832 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2318 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 63.3% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 165 through 206 removed outlier: 3.659A pdb=" N GLY A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 206 " --> pdb=" O HIS A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.656A pdb=" N ILE A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 233 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.532A pdb=" N VAL A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 removed outlier: 4.041A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 312 removed outlier: 3.631A pdb=" N LEU A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 4.013A pdb=" N ALA A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 377 removed outlier: 4.142A pdb=" N MET A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 removed outlier: 4.808A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 430 removed outlier: 3.628A pdb=" N THR A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 455 Processing helix chain 'A' and resid 479 through 499 removed outlier: 4.105A pdb=" N CYS A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS A 484 " --> pdb=" O HIS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 503 removed outlier: 3.867A pdb=" N LYS A 503 " --> pdb=" O SER A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 503' Processing helix chain 'A' and resid 533 through 546 removed outlier: 3.850A pdb=" N ASP A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 removed outlier: 4.419A pdb=" N CYS A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 685 removed outlier: 3.549A pdb=" N SER A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 713 through 734 removed outlier: 3.902A pdb=" N LEU A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 762 Processing helix chain 'A' and resid 770 through 783 removed outlier: 3.623A pdb=" N THR A 783 " --> pdb=" O TRP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 809 removed outlier: 3.619A pdb=" N ILE A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE A 806 " --> pdb=" O ALA A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 852 removed outlier: 3.767A pdb=" N PHE A 838 " --> pdb=" O TYR A 834 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 839 " --> pdb=" O PRO A 835 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 841 " --> pdb=" O TYR A 837 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY A 842 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 876 removed outlier: 3.519A pdb=" N MET A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 891 removed outlier: 3.737A pdb=" N TYR A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 Processing helix chain 'A' and resid 899 through 957 removed outlier: 3.584A pdb=" N LEU A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 967 removed outlier: 3.822A pdb=" N GLU A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 997 removed outlier: 4.494A pdb=" N ASP A 995 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1025 Processing helix chain 'A' and resid 1059 through 1083 removed outlier: 3.806A pdb=" N CYS A1063 " --> pdb=" O TRP A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1126 removed outlier: 4.053A pdb=" N ASN A1118 " --> pdb=" O GLY A1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 Processing helix chain 'B' and resid 89 through 113 removed outlier: 4.171A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.705A pdb=" N ASN B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 137 " --> pdb=" O SER B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 174 through 180 removed outlier: 3.571A pdb=" N PHE B 178 " --> pdb=" O CYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 187 removed outlier: 4.315A pdb=" N GLN B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 230 through 238 removed outlier: 4.074A pdb=" N ILE B 235 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 238 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 313 through 318 removed outlier: 4.349A pdb=" N ARG B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 352 removed outlier: 4.261A pdb=" N SER B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 388 removed outlier: 3.741A pdb=" N ILE B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 417 removed outlier: 5.356A pdb=" N ARG A 411 " --> pdb=" O CYS A 519 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS A 519 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU A 413 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 517 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 422 Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'A' and resid 976 through 979 removed outlier: 4.287A pdb=" N TYR A 976 " --> pdb=" O VAL A1102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1032 through 1038 removed outlier: 7.467A pdb=" N MET A1043 " --> pdb=" O ILE A1035 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR A1037 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR A1041 " --> pdb=" O THR A1037 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A1091 " --> pdb=" O GLN A1133 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE A1132 " --> pdb=" O GLN A1163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 214 removed outlier: 6.424A pdb=" N HIS B 41 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE B 222 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU B 43 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 247 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN B 292 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 248 " --> pdb=" O ASN B 292 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1698 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: 4.14 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1642 1.32 - 1.45: 2690 1.45 - 1.57: 5688 1.57 - 1.69: 5 1.69 - 1.82: 95 Bond restraints: 10120 Sorted by residual: bond pdb=" N VAL A 253 " pdb=" CA VAL A 253 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.21e+00 bond pdb=" N MET A 255 " pdb=" CA MET A 255 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.65e+00 bond pdb=" N THR A 256 " pdb=" CA THR A 256 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.64e+00 bond pdb=" N TRP A 252 " pdb=" CA TRP A 252 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.62e+00 bond pdb=" N THR A 257 " pdb=" CA THR A 257 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.40e+00 ... (remaining 10115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 13531 2.48 - 4.95: 150 4.95 - 7.43: 20 7.43 - 9.91: 2 9.91 - 12.38: 2 Bond angle restraints: 13705 Sorted by residual: angle pdb=" CA LEU A 418 " pdb=" CB LEU A 418 " pdb=" CG LEU A 418 " ideal model delta sigma weight residual 116.30 128.68 -12.38 3.50e+00 8.16e-02 1.25e+01 angle pdb=" CB MET A 741 " pdb=" CG MET A 741 " pdb=" SD MET A 741 " ideal model delta sigma weight residual 112.70 122.84 -10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" CA GLN A1145 " pdb=" CB GLN A1145 " pdb=" CG GLN A1145 " ideal model delta sigma weight residual 114.10 120.33 -6.23 2.00e+00 2.50e-01 9.72e+00 angle pdb=" CA GLU A 950 " pdb=" CB GLU A 950 " pdb=" CG GLU A 950 " ideal model delta sigma weight residual 114.10 120.29 -6.19 2.00e+00 2.50e-01 9.58e+00 ... (remaining 13700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5226 17.56 - 35.12: 653 35.12 - 52.68: 206 52.68 - 70.24: 31 70.24 - 87.80: 15 Dihedral angle restraints: 6131 sinusoidal: 2551 harmonic: 3580 Sorted by residual: dihedral pdb=" CA CYS A 469 " pdb=" C CYS A 469 " pdb=" N VAL A 470 " pdb=" CA VAL A 470 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA MET A1002 " pdb=" C MET A1002 " pdb=" N ASN A1003 " pdb=" CA ASN A1003 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA CYS A 457 " pdb=" C CYS A 457 " pdb=" N LEU A 458 " pdb=" CA LEU A 458 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1265 0.050 - 0.101: 242 0.101 - 0.151: 41 0.151 - 0.202: 6 0.202 - 0.252: 1 Chirality restraints: 1555 Sorted by residual: chirality pdb=" C8 FOK A1301 " pdb=" C7 FOK A1301 " pdb=" C9 FOK A1301 " pdb=" O1 FOK A1301 " both_signs ideal model delta sigma weight residual False 2.90 2.65 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C6 FOK A1301 " pdb=" C5 FOK A1301 " pdb=" C7 FOK A1301 " pdb=" O3 FOK A1301 " both_signs ideal model delta sigma weight residual False -2.28 -2.48 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C7 FOK A1301 " pdb=" C6 FOK A1301 " pdb=" C8 FOK A1301 " pdb=" O4 FOK A1301 " both_signs ideal model delta sigma weight residual False -2.45 -2.64 0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 1552 not shown) Planarity restraints: 1733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 931 " -0.020 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP A 931 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 931 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 931 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 931 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 931 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 931 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 931 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 931 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 931 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 834 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 835 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 835 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 835 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 121 " -0.031 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO B 122 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.027 5.00e-02 4.00e+02 ... (remaining 1730 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 72 2.51 - 3.11: 7486 3.11 - 3.71: 15997 3.71 - 4.30: 21502 4.30 - 4.90: 35140 Nonbonded interactions: 80197 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 1.915 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 2.018 2.170 nonbonded pdb=" O VAL A 758 " pdb=" OG1 THR A 762 " model vdw 2.211 3.040 nonbonded pdb=" O ASP A 191 " pdb=" OG1 THR A 194 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR A1000 " pdb=" OD1 ASN A1003 " model vdw 2.252 3.040 ... (remaining 80192 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.920 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.690 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 0.003 0.037 10120 Z= 0.181 Angle : 0.620 12.382 13705 Z= 0.312 Chirality : 0.041 0.252 1555 Planarity : 0.003 0.049 1733 Dihedral : 17.226 87.803 3807 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.46 % Allowed : 27.73 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.24), residues: 1211 helix: 1.23 (0.20), residues: 690 sheet: -0.13 (0.48), residues: 108 loop : -1.23 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 931 HIS 0.009 0.001 HIS A 399 PHE 0.031 0.002 PHE A 448 TYR 0.020 0.001 TYR A 468 ARG 0.005 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 1.108 Fit side-chains REVERT: A 418 LEU cc_start: 0.8741 (tt) cc_final: 0.8387 (tp) REVERT: B 387 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.4721 (t70) outliers start: 5 outliers final: 3 residues processed: 135 average time/residue: 0.2051 time to fit residues: 41.3775 Evaluate side-chains 129 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 5.9990 chunk 92 optimal weight: 0.0970 chunk 51 optimal weight: 0.0970 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 0.0000 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** A 888 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 = 0.4197 r_free = 0.4197 target = 0.163092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.126789 restraints weight = 18869.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130445 restraints weight = 9668.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.132853 restraints weight = 6470.907| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10120 Z= 0.168 Angle : 0.590 8.696 13705 Z= 0.302 Chirality : 0.041 0.183 1555 Planarity : 0.004 0.043 1733 Dihedral : 5.393 47.961 1439 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.60 % Allowed : 24.58 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.24), residues: 1211 helix: 1.41 (0.19), residues: 723 sheet: 0.02 (0.47), residues: 101 loop : -1.18 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 931 HIS 0.005 0.001 HIS A 399 PHE 0.016 0.001 PHE A 176 TYR 0.015 0.001 TYR A 468 ARG 0.006 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 491 MET cc_start: 0.7569 (mtt) cc_final: 0.7317 (mtt) REVERT: A 856 ASN cc_start: 0.6990 (t0) cc_final: 0.6674 (t0) REVERT: A 879 TYR cc_start: 0.6007 (m-80) cc_final: 0.5039 (m-80) REVERT: A 952 MET cc_start: 0.7435 (ttm) cc_final: 0.7039 (ttt) REVERT: B 194 ASP cc_start: 0.8180 (p0) cc_final: 0.7705 (t0) outliers start: 39 outliers final: 13 residues processed: 175 average time/residue: 0.1996 time to fit residues: 52.3108 Evaluate side-chains 143 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 294 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 115 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.156836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.122056 restraints weight = 19616.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.123317 restraints weight = 10833.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124144 restraints weight = 7760.057| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10120 Z= 0.218 Angle : 0.595 7.773 13705 Z= 0.305 Chirality : 0.042 0.175 1555 Planarity : 0.004 0.040 1733 Dihedral : 4.557 28.674 1431 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.88 % Allowed : 24.68 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.24), residues: 1211 helix: 1.52 (0.19), residues: 722 sheet: 0.06 (0.50), residues: 93 loop : -1.21 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 931 HIS 0.005 0.001 HIS B 149 PHE 0.027 0.002 PHE A 176 TYR 0.022 0.001 TYR A 468 ARG 0.004 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 1.105 Fit side-chains REVERT: A 255 MET cc_start: 0.8134 (mtp) cc_final: 0.7831 (mtt) REVERT: A 406 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7950 (ptm-80) REVERT: A 787 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6757 (ptp-170) REVERT: A 861 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7595 (tt) REVERT: A 879 TYR cc_start: 0.6027 (m-80) cc_final: 0.5066 (m-80) REVERT: B 302 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8277 (mp) outliers start: 42 outliers final: 21 residues processed: 166 average time/residue: 0.1836 time to fit residues: 45.7037 Evaluate side-chains 150 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 302 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS A 949 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.154306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119240 restraints weight = 19462.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.120586 restraints weight = 10639.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.121382 restraints weight = 7742.690| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10120 Z= 0.293 Angle : 0.646 7.297 13705 Z= 0.332 Chirality : 0.044 0.207 1555 Planarity : 0.004 0.041 1733 Dihedral : 4.854 31.027 1431 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.19 % Allowed : 24.21 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.24), residues: 1211 helix: 1.32 (0.19), residues: 727 sheet: 0.07 (0.47), residues: 107 loop : -1.47 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1113 HIS 0.005 0.001 HIS A 402 PHE 0.025 0.002 PHE A 799 TYR 0.025 0.002 TYR A 468 ARG 0.003 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 1.107 Fit side-chains REVERT: A 255 MET cc_start: 0.8206 (mtp) cc_final: 0.7940 (mtt) REVERT: A 406 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7910 (ptm-80) REVERT: A 491 MET cc_start: 0.7823 (mtt) cc_final: 0.7567 (mtt) REVERT: A 787 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7097 (ptp-170) REVERT: A 952 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7447 (ttm) REVERT: A 1139 TYR cc_start: 0.6069 (OUTLIER) cc_final: 0.5462 (p90) REVERT: B 302 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8210 (mp) outliers start: 67 outliers final: 42 residues processed: 179 average time/residue: 0.1817 time to fit residues: 48.9893 Evaluate side-chains 170 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 TYR Chi-restraints excluded: chain A residue 1147 PHE Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 302 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 89 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.156742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.122255 restraints weight = 19132.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.123452 restraints weight = 10393.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.123952 restraints weight = 7545.820| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10120 Z= 0.196 Angle : 0.589 8.164 13705 Z= 0.298 Chirality : 0.041 0.177 1555 Planarity : 0.003 0.040 1733 Dihedral : 4.659 29.799 1431 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.81 % Allowed : 25.88 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.24), residues: 1211 helix: 1.53 (0.19), residues: 727 sheet: -0.15 (0.46), residues: 113 loop : -1.44 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 931 HIS 0.005 0.001 HIS A 399 PHE 0.027 0.002 PHE A 799 TYR 0.019 0.001 TYR A 468 ARG 0.003 0.000 ARG A 926 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 120 time to evaluate : 1.242 Fit side-chains REVERT: A 406 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7812 (ptm-80) REVERT: A 491 MET cc_start: 0.7718 (mtt) cc_final: 0.7465 (mtt) REVERT: A 787 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7222 (ptp-170) REVERT: A 952 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7312 (ttm) REVERT: B 302 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8244 (mp) outliers start: 52 outliers final: 32 residues processed: 160 average time/residue: 0.1691 time to fit residues: 41.7547 Evaluate side-chains 153 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 302 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.154459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119898 restraints weight = 19261.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.121069 restraints weight = 10633.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.121470 restraints weight = 7695.529| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10120 Z= 0.264 Angle : 0.633 8.731 13705 Z= 0.321 Chirality : 0.043 0.173 1555 Planarity : 0.004 0.041 1733 Dihedral : 4.830 31.687 1431 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.55 % Allowed : 24.86 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.24), residues: 1211 helix: 1.41 (0.19), residues: 725 sheet: -0.21 (0.45), residues: 113 loop : -1.55 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1113 HIS 0.005 0.001 HIS A 402 PHE 0.026 0.002 PHE A 799 TYR 0.024 0.002 TYR A 468 ARG 0.003 0.000 ARG A 926 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 122 time to evaluate : 1.176 Fit side-chains REVERT: A 406 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7830 (ptm-80) REVERT: A 491 MET cc_start: 0.7840 (mtt) cc_final: 0.7606 (mtt) REVERT: A 709 MET cc_start: 0.6426 (tpp) cc_final: 0.6148 (tpt) REVERT: A 787 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7315 (ptp-170) REVERT: A 834 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.5121 (m-80) REVERT: A 952 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7402 (ttm) REVERT: A 1139 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5546 (p90) REVERT: B 302 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8229 (mp) REVERT: B 387 HIS cc_start: 0.5943 (OUTLIER) cc_final: 0.5056 (t70) outliers start: 60 outliers final: 41 residues processed: 167 average time/residue: 0.1661 time to fit residues: 43.0906 Evaluate side-chains 165 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 TYR Chi-restraints excluded: chain A residue 1147 PHE Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.156313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.121920 restraints weight = 19457.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.123086 restraints weight = 10322.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.124579 restraints weight = 7238.265| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10120 Z= 0.193 Angle : 0.594 10.120 13705 Z= 0.299 Chirality : 0.041 0.185 1555 Planarity : 0.003 0.040 1733 Dihedral : 4.670 30.857 1431 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.90 % Allowed : 26.34 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.24), residues: 1211 helix: 1.56 (0.19), residues: 725 sheet: -0.17 (0.45), residues: 113 loop : -1.52 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 931 HIS 0.008 0.001 HIS A 399 PHE 0.030 0.002 PHE A 799 TYR 0.019 0.001 TYR A 468 ARG 0.003 0.000 ARG A 926 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 1.164 Fit side-chains REVERT: A 406 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7778 (ptm-80) REVERT: A 787 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7511 (ptp-170) REVERT: A 952 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7319 (ttm) REVERT: A 1139 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5527 (p90) REVERT: B 302 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 387 HIS cc_start: 0.5907 (OUTLIER) cc_final: 0.5039 (t70) outliers start: 53 outliers final: 40 residues processed: 165 average time/residue: 0.1814 time to fit residues: 45.8795 Evaluate side-chains 164 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 TYR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 119 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.156152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122095 restraints weight = 19445.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.123044 restraints weight = 10956.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.124135 restraints weight = 7877.265| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10120 Z= 0.202 Angle : 0.598 9.221 13705 Z= 0.301 Chirality : 0.042 0.189 1555 Planarity : 0.004 0.039 1733 Dihedral : 4.639 30.228 1431 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.36 % Allowed : 25.79 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.24), residues: 1211 helix: 1.56 (0.19), residues: 728 sheet: -0.16 (0.45), residues: 113 loop : -1.48 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 931 HIS 0.006 0.001 HIS A 399 PHE 0.028 0.002 PHE A 799 TYR 0.021 0.001 TYR A 468 ARG 0.005 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 1.180 Fit side-chains REVERT: A 406 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7740 (ptm-80) REVERT: A 709 MET cc_start: 0.6337 (tpp) cc_final: 0.5964 (tpt) REVERT: A 787 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7499 (ptp-170) REVERT: A 952 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7285 (ttm) REVERT: A 1139 TYR cc_start: 0.6391 (OUTLIER) cc_final: 0.5661 (p90) REVERT: B 302 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8291 (mp) REVERT: B 387 HIS cc_start: 0.5944 (OUTLIER) cc_final: 0.5081 (t70) outliers start: 58 outliers final: 43 residues processed: 169 average time/residue: 0.1697 time to fit residues: 44.1603 Evaluate side-chains 167 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 TYR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.155595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121308 restraints weight = 19403.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.122508 restraints weight = 10588.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.123545 restraints weight = 7613.121| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10120 Z= 0.219 Angle : 0.613 8.105 13705 Z= 0.310 Chirality : 0.042 0.180 1555 Planarity : 0.004 0.039 1733 Dihedral : 4.680 31.371 1431 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.90 % Allowed : 26.80 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.24), residues: 1211 helix: 1.49 (0.19), residues: 728 sheet: -0.16 (0.45), residues: 113 loop : -1.50 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 808 HIS 0.005 0.001 HIS A 402 PHE 0.030 0.002 PHE A 799 TYR 0.021 0.001 TYR A 468 ARG 0.005 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 118 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 406 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7762 (ptm-80) REVERT: A 709 MET cc_start: 0.6428 (tpp) cc_final: 0.6092 (tpt) REVERT: A 741 MET cc_start: 0.6401 (mmm) cc_final: 0.4318 (tmm) REVERT: A 787 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7561 (ptp-170) REVERT: A 952 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7329 (ttm) REVERT: A 1139 TYR cc_start: 0.6550 (OUTLIER) cc_final: 0.5852 (p90) REVERT: B 302 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8285 (mp) REVERT: B 387 HIS cc_start: 0.5968 (OUTLIER) cc_final: 0.5108 (t70) outliers start: 53 outliers final: 45 residues processed: 160 average time/residue: 0.1656 time to fit residues: 41.1327 Evaluate side-chains 167 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 TYR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 114 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 0.0040 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 0.0270 chunk 105 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.155450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119140 restraints weight = 19598.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.122497 restraints weight = 10440.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124609 restraints weight = 7108.217| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10120 Z= 0.194 Angle : 0.605 8.073 13705 Z= 0.304 Chirality : 0.042 0.193 1555 Planarity : 0.003 0.039 1733 Dihedral : 4.606 30.620 1431 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.71 % Allowed : 26.62 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.24), residues: 1211 helix: 1.54 (0.19), residues: 730 sheet: 0.05 (0.49), residues: 98 loop : -1.49 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 808 HIS 0.005 0.001 HIS A 402 PHE 0.030 0.002 PHE A 799 TYR 0.019 0.001 TYR A 468 ARG 0.005 0.000 ARG B 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 406 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7745 (ptm-80) REVERT: A 679 LEU cc_start: 0.6634 (tp) cc_final: 0.6349 (tp) REVERT: A 709 MET cc_start: 0.6459 (tpp) cc_final: 0.6121 (tpt) REVERT: A 741 MET cc_start: 0.6323 (mmm) cc_final: 0.4227 (tmm) REVERT: A 787 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7602 (ptp-170) REVERT: A 952 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7249 (ttm) REVERT: A 1139 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.5923 (p90) REVERT: B 302 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8306 (mp) REVERT: B 387 HIS cc_start: 0.5943 (OUTLIER) cc_final: 0.5124 (t70) outliers start: 51 outliers final: 42 residues processed: 166 average time/residue: 0.1637 time to fit residues: 42.3253 Evaluate side-chains 168 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 120 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 TYR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 32 optimal weight: 0.6980 chunk 95 optimal weight: 0.0970 chunk 41 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.156596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121938 restraints weight = 19453.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.123388 restraints weight = 10425.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124871 restraints weight = 7432.724| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10120 Z= 0.180 Angle : 0.599 8.022 13705 Z= 0.300 Chirality : 0.041 0.196 1555 Planarity : 0.003 0.039 1733 Dihedral : 4.543 29.151 1431 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.97 % Allowed : 27.54 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.24), residues: 1211 helix: 1.57 (0.19), residues: 736 sheet: 0.10 (0.49), residues: 98 loop : -1.42 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 808 HIS 0.005 0.001 HIS A 402 PHE 0.031 0.002 PHE A 799 TYR 0.018 0.001 TYR A 468 ARG 0.004 0.000 ARG B 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3486.58 seconds wall clock time: 63 minutes 43.12 seconds (3823.12 seconds total)