Starting phenix.real_space_refine on Mon Jun 9 03:05:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8buz_16252/06_2025/8buz_16252_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8buz_16252/06_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_16252/06_2025/8buz_16252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8buz_16252/06_2025/8buz_16252.map" model { file = "/net/cci-nas-00/data/ceres_data/8buz_16252/06_2025/8buz_16252_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8buz_16252/06_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-5710/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: 7.26, per 1000 atoms: 0.73 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: 2.62 Conformation dependent library (CDL) restraints added in 1.3 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: 0.94 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: 3.20 Time building geometry restraints manager: 3.09 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.050 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.340 ------------------------------------------------------------------------------- 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 10122 Z= 0.142 Angle : 0.620 12.382 13709 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 Details of bonding type rmsd hydrogen bonds : bond 0.21678 ( 580) hydrogen bonds : angle 6.74466 ( 1698) SS BOND : bond 0.00570 ( 2) SS BOND : angle 1.16833 ( 4) covalent geometry : bond 0.00278 (10120) covalent geometry : angle 0.61992 (13705) *********************** 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 : 1.183 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: 0.2037 time to fit residues: 40.4183 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 : 1.093 ------------------------------------------------------------------------------- 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 = 64)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.126790 restraints weight = 18869.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.130509 restraints weight = 9667.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.132865 restraints weight = 6432.084| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 10122 Z= 0.129 Angle : 0.590 8.696 13709 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 Details of bonding type rmsd hydrogen bonds : bond 0.05192 ( 580) hydrogen bonds : angle 4.43316 ( 1698) SS BOND : bond 0.00470 ( 2) SS BOND : angle 0.75991 ( 4) covalent geometry : bond 0.00259 (10120) covalent geometry : angle 0.58988 (13705) *********************** 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 : 1.250 Fit side-chains revert: symmetry clash REVERT: A 491 MET cc_start: 0.7573 (mtt) cc_final: 0.7321 (mtt) REVERT: A 856 ASN cc_start: 0.7008 (t0) cc_final: 0.6689 (t0) REVERT: A 879 TYR cc_start: 0.6008 (m-80) cc_final: 0.5039 (m-80) REVERT: A 952 MET cc_start: 0.7436 (ttm) cc_final: 0.7043 (ttt) REVERT: B 194 ASP cc_start: 0.8178 (p0) cc_final: 0.7706 (t0) outliers start: 39 outliers final: 13 residues processed: 175 average time/residue: 0.1972 time to fit residues: 51.1285 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 : 1.195 ------------------------------------------------------------------------------- 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: 0.5980 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.157876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121409 restraints weight = 19565.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.124790 restraints weight = 10468.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.127005 restraints weight = 7168.034| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10122 Z= 0.136 Angle : 0.582 7.964 13709 Z= 0.298 Chirality : 0.041 0.174 1555 Planarity : 0.003 0.040 1733 Dihedral : 4.496 28.296 1431 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.51 % Allowed : 24.58 % Favored : 71.90 % 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: 0.84 (0.24), residues: 1211 helix: 1.54 (0.19), residues: 724 sheet: 0.17 (0.50), residues: 92 loop : -1.19 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 931 HIS 0.005 0.001 HIS B 149 PHE 0.026 0.002 PHE A 176 TYR 0.020 0.001 TYR A 468 ARG 0.003 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.05029 ( 580) hydrogen bonds : angle 4.26889 ( 1698) SS BOND : bond 0.00430 ( 2) SS BOND : angle 1.03296 ( 4) covalent geometry : bond 0.00297 (10120) covalent geometry : angle 0.58219 (13705) *********************** 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 175 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 1.185 Fit side-chains REVERT: A 255 MET cc_start: 0.8221 (mtp) cc_final: 0.7875 (mtt) REVERT: A 406 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7919 (ptm-80) REVERT: A 787 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.6756 (ptp-170) REVERT: A 861 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7524 (tt) REVERT: A 879 TYR cc_start: 0.6042 (m-80) cc_final: 0.5093 (m-80) REVERT: B 194 ASP cc_start: 0.8175 (p0) cc_final: 0.7720 (t0) REVERT: B 302 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8296 (mp) outliers start: 38 outliers final: 18 residues processed: 165 average time/residue: 0.1916 time to fit residues: 47.1520 Evaluate side-chains 149 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 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 1046 SER 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 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: 0.4980 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 85 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 582 HIS A 781 ASN A 949 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.158157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.126084 restraints weight = 19448.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.126964 restraints weight = 11274.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.127569 restraints weight = 9714.084| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10122 Z= 0.124 Angle : 0.571 9.018 13709 Z= 0.289 Chirality : 0.041 0.176 1555 Planarity : 0.003 0.038 1733 Dihedral : 4.410 25.327 1431 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.07 % Allowed : 25.05 % Favored : 70.89 % 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: 0.88 (0.24), residues: 1211 helix: 1.60 (0.19), residues: 726 sheet: 0.17 (0.50), residues: 92 loop : -1.25 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 931 HIS 0.004 0.001 HIS A 399 PHE 0.025 0.001 PHE A 799 TYR 0.025 0.001 TYR B 190 ARG 0.004 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 580) hydrogen bonds : angle 4.09514 ( 1698) SS BOND : bond 0.00363 ( 2) SS BOND : angle 1.10557 ( 4) covalent geometry : bond 0.00265 (10120) covalent geometry : angle 0.57077 (13705) *********************** 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 183 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.188 Fit side-chains REVERT: A 406 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7860 (ptm-80) REVERT: A 787 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7186 (ptp-170) REVERT: A 861 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7689 (tt) REVERT: A 879 TYR cc_start: 0.5894 (m-80) cc_final: 0.4986 (m-80) REVERT: A 952 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7189 (ttm) outliers start: 44 outliers final: 25 residues processed: 172 average time/residue: 0.1805 time to fit residues: 46.9543 Evaluate side-chains 158 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 679 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 861 LEU Chi-restraints excluded: chain A residue 927 LEU 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 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 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 379 CYS 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: 0.8980 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 326 GLN ** 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 = 0.4124 r_free = 0.4124 target = 0.157418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125191 restraints weight = 19389.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.126473 restraints weight = 11136.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126984 restraints weight = 9086.469| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10122 Z= 0.128 Angle : 0.574 8.906 13709 Z= 0.289 Chirality : 0.041 0.172 1555 Planarity : 0.003 0.037 1733 Dihedral : 4.446 24.995 1431 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.71 % Allowed : 25.14 % Favored : 70.15 % 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: 0.92 (0.25), residues: 1211 helix: 1.65 (0.19), residues: 726 sheet: -0.11 (0.46), residues: 107 loop : -1.22 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 931 HIS 0.004 0.001 HIS A 402 PHE 0.026 0.002 PHE A 799 TYR 0.020 0.001 TYR A 468 ARG 0.003 0.000 ARG A 926 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 580) hydrogen bonds : angle 4.01899 ( 1698) SS BOND : bond 0.00418 ( 2) SS BOND : angle 1.29045 ( 4) covalent geometry : bond 0.00279 (10120) covalent geometry : angle 0.57381 (13705) *********************** 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 179 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 1.091 Fit side-chains REVERT: A 406 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7890 (ptm-80) REVERT: A 787 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7612 (ptp-170) REVERT: A 861 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7692 (tt) REVERT: A 952 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7268 (ttm) REVERT: B 387 HIS cc_start: 0.5929 (OUTLIER) cc_final: 0.5675 (t70) outliers start: 51 outliers final: 31 residues processed: 164 average time/residue: 0.1853 time to fit residues: 45.1500 Evaluate side-chains 161 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 301 THR 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 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 679 LEU 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 861 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET 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 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.156998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120581 restraints weight = 19437.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123965 restraints weight = 10245.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126158 restraints weight = 6984.703| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10122 Z= 0.132 Angle : 0.584 9.281 13709 Z= 0.295 Chirality : 0.041 0.176 1555 Planarity : 0.003 0.037 1733 Dihedral : 4.470 25.800 1431 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.90 % Allowed : 24.77 % Favored : 70.33 % 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: 0.90 (0.25), residues: 1211 helix: 1.64 (0.19), residues: 726 sheet: -0.14 (0.46), residues: 107 loop : -1.23 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 931 HIS 0.004 0.001 HIS A 402 PHE 0.027 0.002 PHE A 799 TYR 0.019 0.001 TYR A 468 ARG 0.003 0.000 ARG A 926 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 580) hydrogen bonds : angle 4.01206 ( 1698) SS BOND : bond 0.00493 ( 2) SS BOND : angle 1.22481 ( 4) covalent geometry : bond 0.00291 (10120) covalent geometry : angle 0.58333 (13705) *********************** 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 179 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 1.218 Fit side-chains REVERT: A 350 GLN cc_start: 0.8074 (mm110) cc_final: 0.7869 (mm110) REVERT: A 406 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7928 (ptm-80) REVERT: A 709 MET cc_start: 0.6128 (tpp) cc_final: 0.5849 (tpt) REVERT: A 787 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7492 (ptp-170) REVERT: A 952 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7246 (ttm) REVERT: A 1139 TYR cc_start: 0.5994 (OUTLIER) cc_final: 0.5279 (p90) REVERT: B 387 HIS cc_start: 0.5928 (OUTLIER) cc_final: 0.5639 (t70) outliers start: 53 outliers final: 38 residues processed: 163 average time/residue: 0.1859 time to fit residues: 47.0865 Evaluate side-chains 166 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 301 THR Chi-restraints excluded: chain A residue 363 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 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 679 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 889 LEU Chi-restraints excluded: chain A residue 927 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 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 57 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN 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: 0.9990 chunk 8 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 781 ASN 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 = 0.156356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.124173 restraints weight = 19616.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125452 restraints weight = 11411.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.125985 restraints weight = 9080.119| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10122 Z= 0.141 Angle : 0.593 8.449 13709 Z= 0.299 Chirality : 0.042 0.179 1555 Planarity : 0.003 0.038 1733 Dihedral : 4.526 26.824 1431 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.71 % Allowed : 25.14 % Favored : 70.15 % 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: 0.98 (0.25), residues: 1211 helix: 1.68 (0.19), residues: 725 sheet: -0.03 (0.46), residues: 113 loop : -1.20 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 808 HIS 0.005 0.001 HIS A 402 PHE 0.028 0.002 PHE A 799 TYR 0.021 0.001 TYR A 468 ARG 0.003 0.000 ARG A 926 Details of bonding type rmsd hydrogen bonds : bond 0.04766 ( 580) hydrogen bonds : angle 4.01722 ( 1698) SS BOND : bond 0.00720 ( 2) SS BOND : angle 1.04850 ( 4) covalent geometry : bond 0.00317 (10120) covalent geometry : angle 0.59265 (13705) *********************** 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 176 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 1.335 Fit side-chains REVERT: A 406 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7851 (ptm-80) REVERT: A 787 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7746 (ptp-170) REVERT: A 952 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7298 (ttm) REVERT: A 1139 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5402 (p90) REVERT: B 387 HIS cc_start: 0.5968 (OUTLIER) cc_final: 0.5695 (t70) outliers start: 51 outliers final: 35 residues processed: 165 average time/residue: 0.1780 time to fit residues: 44.7643 Evaluate side-chains 156 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 301 THR 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 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 889 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 927 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 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 60 MET 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 387 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 0.0040 chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.0000 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 781 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.158320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126395 restraints weight = 19573.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127589 restraints weight = 11677.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128051 restraints weight = 9367.595| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10122 Z= 0.117 Angle : 0.575 9.489 13709 Z= 0.289 Chirality : 0.041 0.196 1555 Planarity : 0.003 0.036 1733 Dihedral : 4.391 25.469 1431 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.60 % Allowed : 26.62 % Favored : 69.78 % 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: 1.02 (0.25), residues: 1211 helix: 1.74 (0.19), residues: 728 sheet: 0.07 (0.46), residues: 107 loop : -1.26 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 931 HIS 0.005 0.001 HIS A 402 PHE 0.030 0.001 PHE A 799 TYR 0.017 0.001 TYR A 468 ARG 0.003 0.000 ARG A 926 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 580) hydrogen bonds : angle 3.93978 ( 1698) SS BOND : bond 0.00676 ( 2) SS BOND : angle 0.76845 ( 4) covalent geometry : bond 0.00248 (10120) covalent geometry : angle 0.57503 (13705) *********************** 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 175 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 1.211 Fit side-chains REVERT: A 373 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7325 (tm-30) REVERT: A 406 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7881 (ptm-80) REVERT: A 709 MET cc_start: 0.6080 (tpp) cc_final: 0.5735 (tpt) REVERT: A 741 MET cc_start: 0.6323 (mmm) cc_final: 0.4225 (tmm) REVERT: A 787 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7859 (ptp-170) REVERT: A 952 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7185 (ttm) REVERT: B 387 HIS cc_start: 0.5920 (OUTLIER) cc_final: 0.5119 (t70) outliers start: 39 outliers final: 29 residues processed: 164 average time/residue: 0.1837 time to fit residues: 45.3706 Evaluate side-chains 158 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 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 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 952 MET 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 153 LEU 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 294 GLN 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: 0.8980 chunk 34 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 0.0070 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.158072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.121673 restraints weight = 19617.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.125051 restraints weight = 10313.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.127233 restraints weight = 7014.086| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10122 Z= 0.124 Angle : 0.587 8.501 13709 Z= 0.295 Chirality : 0.042 0.186 1555 Planarity : 0.003 0.037 1733 Dihedral : 4.388 25.079 1431 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.88 % Allowed : 26.52 % 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: 0.98 (0.25), residues: 1211 helix: 1.69 (0.19), residues: 727 sheet: 0.03 (0.46), residues: 112 loop : -1.24 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 808 HIS 0.004 0.001 HIS A 402 PHE 0.030 0.002 PHE A 799 TYR 0.018 0.001 TYR A 468 ARG 0.008 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 580) hydrogen bonds : angle 3.93606 ( 1698) SS BOND : bond 0.00677 ( 2) SS BOND : angle 0.93703 ( 4) covalent geometry : bond 0.00273 (10120) covalent geometry : angle 0.58691 (13705) *********************** 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 168 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 1.345 Fit side-chains REVERT: A 373 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 406 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7836 (ptm-80) REVERT: A 709 MET cc_start: 0.6123 (tpp) cc_final: 0.5803 (tpt) REVERT: A 741 MET cc_start: 0.6256 (mmm) cc_final: 0.4166 (tmm) REVERT: A 787 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7720 (ptp-170) REVERT: A 952 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7173 (ttm) REVERT: B 387 HIS cc_start: 0.5936 (OUTLIER) cc_final: 0.5133 (t70) outliers start: 42 outliers final: 32 residues processed: 159 average time/residue: 0.2043 time to fit residues: 50.6631 Evaluate side-chains 160 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 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 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 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 927 LEU Chi-restraints excluded: chain A residue 952 MET 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 60 MET 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 287 VAL Chi-restraints excluded: chain B residue 294 GLN 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: 0.5980 chunk 95 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 0.0370 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.158004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121386 restraints weight = 19598.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.124779 restraints weight = 10482.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.127002 restraints weight = 7136.405| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10122 Z= 0.130 Angle : 0.597 8.230 13709 Z= 0.300 Chirality : 0.042 0.190 1555 Planarity : 0.003 0.041 1733 Dihedral : 4.443 25.388 1431 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.60 % Allowed : 27.36 % Favored : 69.04 % 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: 0.93 (0.24), residues: 1211 helix: 1.64 (0.19), residues: 727 sheet: 0.01 (0.45), residues: 112 loop : -1.22 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 808 HIS 0.009 0.001 HIS A 399 PHE 0.032 0.002 PHE A 799 TYR 0.019 0.001 TYR A 468 ARG 0.008 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 580) hydrogen bonds : angle 3.98718 ( 1698) SS BOND : bond 0.00807 ( 2) SS BOND : angle 0.75197 ( 4) covalent geometry : bond 0.00290 (10120) covalent geometry : angle 0.59656 (13705) ********************** 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 163 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 1.096 Fit side-chains REVERT: A 305 GLN cc_start: 0.6749 (pp30) cc_final: 0.5776 (tp40) REVERT: A 373 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7364 (tm-30) REVERT: A 406 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7841 (ptm-80) REVERT: A 709 MET cc_start: 0.6244 (tpp) cc_final: 0.5963 (tpt) REVERT: A 741 MET cc_start: 0.6220 (mmm) cc_final: 0.4224 (tmm) REVERT: A 787 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7686 (ptp-170) REVERT: A 952 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7231 (ttm) REVERT: A 1139 TYR cc_start: 0.6208 (OUTLIER) cc_final: 0.5420 (p90) REVERT: B 387 HIS cc_start: 0.5927 (OUTLIER) cc_final: 0.5133 (t70) outliers start: 39 outliers final: 32 residues processed: 153 average time/residue: 0.1739 time to fit residues: 40.4289 Evaluate side-chains 156 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 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 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 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 927 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 952 MET 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 60 MET 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 287 VAL Chi-restraints excluded: chain B residue 294 GLN 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: 0.8980 chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 0.0370 chunk 83 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 972 ASN ** A1145 GLN ** 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 = 0.4132 r_free = 0.4132 target = 0.158129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.126122 restraints weight = 19529.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.127299 restraints weight = 11641.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.127708 restraints weight = 9375.647| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10122 Z= 0.124 Angle : 0.587 7.992 13709 Z= 0.295 Chirality : 0.042 0.180 1555 Planarity : 0.003 0.038 1733 Dihedral : 4.408 25.314 1431 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.51 % Allowed : 27.26 % Favored : 69.22 % 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: 0.97 (0.24), residues: 1211 helix: 1.67 (0.19), residues: 727 sheet: -0.01 (0.45), residues: 112 loop : -1.23 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 808 HIS 0.008 0.001 HIS A 399 PHE 0.029 0.002 PHE A 799 TYR 0.019 0.001 TYR A 468 ARG 0.008 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 580) hydrogen bonds : angle 3.95177 ( 1698) SS BOND : bond 0.00653 ( 2) SS BOND : angle 1.02908 ( 4) covalent geometry : bond 0.00274 (10120) covalent geometry : angle 0.58718 (13705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3903.00 seconds wall clock time: 68 minutes 37.16 seconds (4117.16 seconds total)