Starting phenix.real_space_refine on Sun Dec 29 08:44:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8buz_16252/12_2024/8buz_16252_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8buz_16252/12_2024/8buz_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_16252/12_2024/8buz_16252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8buz_16252/12_2024/8buz_16252.map" model { file = "/net/cci-nas-00/data/ceres_data/8buz_16252/12_2024/8buz_16252_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8buz_16252/12_2024/8buz_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-5532/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: 6.89, per 1000 atoms: 0.69 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: 2.84 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: 0.99 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: 3.15 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1642 1.32 - 1.45: 2690 1.45 - 1.57: 5688 1.57 - 1.69: 5 1.69 - 1.82: 95 Bond restraints: 10120 Sorted by residual: bond pdb=" N VAL A 253 " pdb=" CA VAL A 253 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.21e+00 bond pdb=" N MET A 255 " pdb=" CA MET A 255 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.65e+00 bond pdb=" N THR A 256 " pdb=" CA THR A 256 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.64e+00 bond pdb=" N TRP A 252 " pdb=" CA TRP A 252 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.62e+00 bond pdb=" N THR A 257 " pdb=" CA THR A 257 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.40e+00 ... (remaining 10115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 13531 2.48 - 4.95: 150 4.95 - 7.43: 20 7.43 - 9.91: 2 9.91 - 12.38: 2 Bond angle restraints: 13705 Sorted by residual: angle pdb=" CA LEU A 418 " pdb=" CB LEU A 418 " pdb=" CG LEU A 418 " ideal model delta sigma weight residual 116.30 128.68 -12.38 3.50e+00 8.16e-02 1.25e+01 angle pdb=" CB MET A 741 " pdb=" CG MET A 741 " pdb=" SD MET A 741 " ideal model delta sigma weight residual 112.70 122.84 -10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" CA GLN A1145 " pdb=" CB GLN A1145 " pdb=" CG GLN A1145 " ideal model delta sigma weight residual 114.10 120.33 -6.23 2.00e+00 2.50e-01 9.72e+00 angle pdb=" CA GLU A 950 " pdb=" CB GLU A 950 " pdb=" CG GLU A 950 " ideal model delta sigma weight residual 114.10 120.29 -6.19 2.00e+00 2.50e-01 9.58e+00 ... (remaining 13700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5226 17.56 - 35.12: 653 35.12 - 52.68: 206 52.68 - 70.24: 31 70.24 - 87.80: 15 Dihedral angle restraints: 6131 sinusoidal: 2551 harmonic: 3580 Sorted by residual: dihedral pdb=" CA CYS A 469 " pdb=" C CYS A 469 " pdb=" N VAL A 470 " pdb=" CA VAL A 470 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA MET A1002 " pdb=" C MET A1002 " pdb=" N ASN A1003 " pdb=" CA ASN A1003 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA CYS A 457 " pdb=" C CYS A 457 " pdb=" N LEU A 458 " pdb=" CA LEU A 458 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1265 0.050 - 0.101: 242 0.101 - 0.151: 41 0.151 - 0.202: 6 0.202 - 0.252: 1 Chirality restraints: 1555 Sorted by residual: chirality pdb=" C8 FOK A1301 " pdb=" C7 FOK A1301 " pdb=" C9 FOK A1301 " pdb=" O1 FOK A1301 " both_signs ideal model delta sigma weight residual False 2.90 2.65 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C6 FOK A1301 " pdb=" C5 FOK A1301 " pdb=" C7 FOK A1301 " pdb=" O3 FOK A1301 " both_signs ideal model delta sigma weight residual False -2.28 -2.48 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C7 FOK A1301 " pdb=" C6 FOK A1301 " pdb=" C8 FOK A1301 " pdb=" O4 FOK A1301 " both_signs ideal model delta sigma weight residual False -2.45 -2.64 0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 1552 not shown) Planarity restraints: 1733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 931 " -0.020 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP A 931 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 931 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 931 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 931 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 931 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 931 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 931 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 931 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 931 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 834 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 835 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 835 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 835 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 121 " -0.031 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO B 122 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.027 5.00e-02 4.00e+02 ... (remaining 1730 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 72 2.51 - 3.11: 7486 3.11 - 3.71: 15997 3.71 - 4.30: 21502 4.30 - 4.90: 35140 Nonbonded interactions: 80197 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 1.915 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 2.018 2.170 nonbonded pdb=" O VAL A 758 " pdb=" OG1 THR A 762 " model vdw 2.211 3.040 nonbonded pdb=" O ASP A 191 " pdb=" OG1 THR A 194 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR A1000 " pdb=" OD1 ASN A1003 " model vdw 2.252 3.040 ... (remaining 80192 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.770 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.030 Find NCS groups from input model: 0.100 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10120 Z= 0.181 Angle : 0.620 12.382 13705 Z= 0.312 Chirality : 0.041 0.252 1555 Planarity : 0.003 0.049 1733 Dihedral : 17.226 87.803 3807 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.46 % Allowed : 27.73 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1211 helix: 1.23 (0.20), residues: 690 sheet: -0.13 (0.48), residues: 108 loop : -1.23 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 931 HIS 0.009 0.001 HIS A 399 PHE 0.031 0.002 PHE A 448 TYR 0.020 0.001 TYR A 468 ARG 0.005 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 1.161 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: 0.2015 time to fit residues: 40.3309 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 : 0.998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10120 Z= 0.168 Angle : 0.590 8.696 13705 Z= 0.302 Chirality : 0.041 0.183 1555 Planarity : 0.004 0.043 1733 Dihedral : 5.393 47.961 1439 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.60 % Allowed : 24.58 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1211 helix: 1.41 (0.19), residues: 723 sheet: 0.02 (0.47), residues: 101 loop : -1.18 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 931 HIS 0.005 0.001 HIS A 399 PHE 0.016 0.001 PHE A 176 TYR 0.015 0.001 TYR A 468 ARG 0.006 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 491 MET cc_start: 0.7161 (mtt) cc_final: 0.6924 (mtt) REVERT: A 856 ASN cc_start: 0.7608 (t0) cc_final: 0.7132 (t0) REVERT: A 879 TYR cc_start: 0.5894 (m-80) cc_final: 0.5105 (m-80) REVERT: A 952 MET cc_start: 0.7415 (ttm) cc_final: 0.7027 (ttt) REVERT: B 194 ASP cc_start: 0.8154 (p0) cc_final: 0.7763 (t0) outliers start: 39 outliers final: 13 residues processed: 175 average time/residue: 0.2035 time to fit residues: 52.5373 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 : 1.119 ------------------------------------------------------------------------------- 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 61 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 0.0570 chunk 110 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10120 Z= 0.186 Angle : 0.580 8.104 13705 Z= 0.296 Chirality : 0.041 0.173 1555 Planarity : 0.003 0.040 1733 Dihedral : 4.477 28.138 1431 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.70 % Allowed : 24.58 % Favored : 71.72 % 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: 0.82 (0.24), residues: 1211 helix: 1.53 (0.19), residues: 725 sheet: 0.17 (0.50), residues: 92 loop : -1.24 (0.32), residues: 394 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 0.027 0.002 PHE A 176 TYR 0.020 0.001 TYR A 468 ARG 0.004 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 1.067 Fit side-chains REVERT: A 406 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8006 (ptm-80) REVERT: A 787 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7194 (ptp-170) REVERT: A 861 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7726 (tt) REVERT: A 879 TYR cc_start: 0.5896 (m-80) cc_final: 0.5159 (m-80) REVERT: B 194 ASP cc_start: 0.8134 (p0) cc_final: 0.7819 (t0) REVERT: B 302 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8292 (mp) outliers start: 40 outliers final: 18 residues processed: 173 average time/residue: 0.1927 time to fit residues: 49.5587 Evaluate side-chains 150 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 385 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 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 83 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN A 582 HIS ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10120 Z= 0.231 Angle : 0.604 8.480 13705 Z= 0.307 Chirality : 0.042 0.177 1555 Planarity : 0.004 0.039 1733 Dihedral : 4.570 26.744 1431 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.27 % Allowed : 23.84 % 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: 0.80 (0.24), residues: 1211 helix: 1.55 (0.19), residues: 722 sheet: -0.09 (0.46), residues: 107 loop : -1.25 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 931 HIS 0.004 0.001 HIS A 399 PHE 0.025 0.002 PHE A 799 TYR 0.021 0.001 TYR A 468 ARG 0.003 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 129 time to evaluate : 1.131 Fit side-chains REVERT: A 406 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7983 (ptm-80) REVERT: A 787 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7524 (ptp-170) REVERT: A 861 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7810 (tt) REVERT: A 952 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7273 (ttm) REVERT: B 302 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8260 (mp) outliers start: 57 outliers final: 35 residues processed: 169 average time/residue: 0.1982 time to fit residues: 50.6629 Evaluate side-chains 161 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 339 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 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 851 VAL 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 933 VAL Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 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 107 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 302 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.0570 chunk 100 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.0050 overall best weight: 0.5314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 403 GLN A 781 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10120 Z= 0.166 Angle : 0.562 7.987 13705 Z= 0.285 Chirality : 0.040 0.174 1555 Planarity : 0.003 0.038 1733 Dihedral : 4.438 25.766 1431 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.97 % Allowed : 26.34 % Favored : 69.69 % 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 (0.24), residues: 1211 helix: 1.67 (0.19), residues: 726 sheet: 0.05 (0.50), residues: 92 loop : -1.27 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 931 HIS 0.004 0.001 HIS A 402 PHE 0.027 0.002 PHE A 799 TYR 0.018 0.001 TYR A 468 ARG 0.004 0.000 ARG A 926 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.116 Fit side-chains REVERT: A 406 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7976 (ptm-80) REVERT: A 787 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7802 (ptp-170) REVERT: A 861 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7794 (tt) REVERT: A 952 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7220 (ttm) REVERT: B 387 HIS cc_start: 0.5753 (OUTLIER) cc_final: 0.4854 (t70) outliers start: 43 outliers final: 24 residues processed: 164 average time/residue: 0.1822 time to fit residues: 45.0730 Evaluate side-chains 152 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 PHE 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 457 CYS Chi-restraints excluded: chain A residue 458 LEU 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 0.0020 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10120 Z= 0.170 Angle : 0.575 9.273 13705 Z= 0.290 Chirality : 0.041 0.174 1555 Planarity : 0.003 0.036 1733 Dihedral : 4.431 25.187 1431 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.07 % Allowed : 26.16 % 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: 0.94 (0.25), residues: 1211 helix: 1.67 (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 0.010 0.001 TRP A 931 HIS 0.004 0.001 HIS A 402 PHE 0.028 0.002 PHE A 799 TYR 0.018 0.001 TYR A 468 ARG 0.003 0.000 ARG B 127 *********************** 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 172 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 1.162 Fit side-chains REVERT: A 406 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7977 (ptm-80) REVERT: A 787 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7889 (ptp-170) REVERT: A 861 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7805 (tt) REVERT: A 952 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7225 (ttm) REVERT: A 1139 TYR cc_start: 0.5774 (OUTLIER) cc_final: 0.5119 (p90) REVERT: B 387 HIS cc_start: 0.5780 (OUTLIER) cc_final: 0.4902 (t70) outliers start: 44 outliers final: 27 residues processed: 157 average time/residue: 0.1818 time to fit residues: 43.5291 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 : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR 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 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 861 LEU Chi-restraints excluded: chain A residue 871 TYR 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 1139 TYR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER 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 13 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10120 Z= 0.181 Angle : 0.580 8.618 13705 Z= 0.291 Chirality : 0.041 0.185 1555 Planarity : 0.003 0.036 1733 Dihedral : 4.419 25.429 1431 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.34 % Allowed : 25.97 % Favored : 69.69 % 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: 1.03 (0.25), residues: 1211 helix: 1.75 (0.19), residues: 727 sheet: -0.12 (0.46), residues: 107 loop : -1.19 (0.33), residues: 377 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 0.029 0.002 PHE A 799 TYR 0.019 0.001 TYR A 468 ARG 0.003 0.000 ARG B 127 *********************** 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 172 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 0.972 Fit side-chains REVERT: A 406 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8000 (ptm-80) REVERT: A 709 MET cc_start: 0.6076 (tpp) cc_final: 0.5838 (tpt) REVERT: A 741 MET cc_start: 0.6204 (mmm) cc_final: 0.4167 (tmm) REVERT: A 787 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7924 (ptp-170) REVERT: A 861 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7824 (tt) REVERT: A 952 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7233 (ttm) REVERT: A 1139 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.5210 (p90) REVERT: B 387 HIS cc_start: 0.5784 (OUTLIER) cc_final: 0.4938 (t70) outliers start: 47 outliers final: 31 residues processed: 160 average time/residue: 0.1795 time to fit residues: 43.5358 Evaluate side-chains 162 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 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 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 861 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 0.0980 chunk 35 optimal weight: 0.4980 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10120 Z= 0.151 Angle : 0.561 7.411 13705 Z= 0.283 Chirality : 0.041 0.202 1555 Planarity : 0.003 0.035 1733 Dihedral : 4.298 24.012 1431 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.23 % Allowed : 27.36 % Favored : 69.41 % 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: 1.08 (0.25), residues: 1211 helix: 1.79 (0.19), residues: 728 sheet: -0.03 (0.46), residues: 102 loop : -1.21 (0.33), residues: 381 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 0.031 0.001 PHE A 799 TYR 0.016 0.001 TYR A 468 ARG 0.004 0.000 ARG B 127 *********************** 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 172 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.144 Fit side-chains REVERT: A 406 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7965 (ptm-80) REVERT: A 741 MET cc_start: 0.6139 (mmm) cc_final: 0.4102 (tmm) REVERT: A 787 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8021 (ptp-170) REVERT: A 861 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7779 (tt) REVERT: A 952 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7075 (ttm) REVERT: B 387 HIS cc_start: 0.5723 (OUTLIER) cc_final: 0.4923 (t70) outliers start: 35 outliers final: 27 residues processed: 161 average time/residue: 0.1892 time to fit residues: 45.7227 Evaluate side-chains 157 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 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 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 861 LEU 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 1151 TYR Chi-restraints excluded: chain A residue 1161 SER 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 112 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.0030 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10120 Z= 0.195 Angle : 0.599 7.307 13705 Z= 0.303 Chirality : 0.042 0.191 1555 Planarity : 0.003 0.036 1733 Dihedral : 4.420 24.915 1431 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.79 % Allowed : 26.80 % Favored : 69.41 % 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: 0.96 (0.25), residues: 1211 helix: 1.67 (0.19), residues: 728 sheet: -0.10 (0.46), residues: 107 loop : -1.19 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 931 HIS 0.004 0.001 HIS B 149 PHE 0.030 0.002 PHE A 799 TYR 0.021 0.001 TYR A 468 ARG 0.007 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 1.170 Fit side-chains REVERT: A 406 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8010 (ptm-80) REVERT: A 741 MET cc_start: 0.6150 (mmm) cc_final: 0.4141 (tmm) REVERT: A 787 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8027 (ptp-170) REVERT: A 795 ILE cc_start: 0.8158 (tt) cc_final: 0.7920 (tt) REVERT: A 861 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7779 (tt) REVERT: A 952 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7220 (ttm) REVERT: A 1139 TYR cc_start: 0.5913 (OUTLIER) cc_final: 0.5144 (p90) REVERT: B 387 HIS cc_start: 0.5757 (OUTLIER) cc_final: 0.4947 (t70) outliers start: 41 outliers final: 30 residues processed: 152 average time/residue: 0.1931 time to fit residues: 44.5443 Evaluate side-chains 158 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 861 LEU 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 1139 TYR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER 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 70 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10120 Z= 0.204 Angle : 0.597 6.977 13705 Z= 0.303 Chirality : 0.042 0.197 1555 Planarity : 0.003 0.042 1733 Dihedral : 4.475 26.044 1431 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.51 % Allowed : 27.54 % Favored : 68.95 % 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: 0.91 (0.24), residues: 1211 helix: 1.63 (0.19), residues: 728 sheet: -0.10 (0.46), residues: 107 loop : -1.22 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 931 HIS 0.009 0.001 HIS A 399 PHE 0.031 0.002 PHE A 799 TYR 0.016 0.001 TYR A 468 ARG 0.008 0.000 ARG B 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.079 Fit side-chains REVERT: A 406 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7961 (ptm-80) REVERT: A 491 MET cc_start: 0.7223 (mtt) cc_final: 0.6980 (mtt) REVERT: A 741 MET cc_start: 0.6156 (mmm) cc_final: 0.4179 (tmm) REVERT: A 787 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8023 (ptp-170) REVERT: A 861 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7785 (tt) REVERT: A 952 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7250 (ttm) REVERT: A 1139 TYR cc_start: 0.6071 (OUTLIER) cc_final: 0.5306 (p90) REVERT: B 387 HIS cc_start: 0.5832 (OUTLIER) cc_final: 0.5019 (t70) outliers start: 38 outliers final: 29 residues processed: 152 average time/residue: 0.1769 time to fit residues: 40.9165 Evaluate side-chains 153 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 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 861 LEU 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 1139 TYR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER 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 29 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.158693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.126770 restraints weight = 19294.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.127462 restraints weight = 11273.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.128148 restraints weight = 9766.172| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10120 Z= 0.173 Angle : 0.579 7.043 13705 Z= 0.293 Chirality : 0.042 0.201 1555 Planarity : 0.003 0.038 1733 Dihedral : 4.390 25.352 1431 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.42 % Allowed : 27.54 % 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: 0.98 (0.24), residues: 1211 helix: 1.70 (0.19), residues: 728 sheet: -0.09 (0.46), residues: 107 loop : -1.21 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 931 HIS 0.008 0.001 HIS A 399 PHE 0.029 0.002 PHE A 799 TYR 0.017 0.001 TYR A 468 ARG 0.007 0.000 ARG B 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.20 seconds wall clock time: 41 minutes 12.73 seconds (2472.73 seconds total)