Starting phenix.real_space_refine on Sun Dec 29 13:34:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dd7_27335/12_2024/8dd7_27335.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dd7_27335/12_2024/8dd7_27335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dd7_27335/12_2024/8dd7_27335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dd7_27335/12_2024/8dd7_27335.map" model { file = "/net/cci-nas-00/data/ceres_data/8dd7_27335/12_2024/8dd7_27335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dd7_27335/12_2024/8dd7_27335.cif" } resolution = 3.3 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 C 6633 2.51 5 N 1780 2.21 5 O 1889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4192 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 26, 'TRANS': 489} Chain: "B" Number of atoms: 6125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 6125 Classifications: {'peptide': 759} Link IDs: {'PTRANS': 29, 'TRANS': 729} Chain breaks: 4 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N CYS A 296 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS A 296 " occ=0.75 Time building chain proxies: 6.45, per 1000 atoms: 0.62 Number of scatterers: 10370 At special positions: 0 Unit cell: (87.72, 99.072, 145.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 2 15.00 O 1889 8.00 N 1780 7.00 C 6633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 65.6% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 53 through 75 Processing helix chain 'A' and resid 87 through 99 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 157 through 169 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 213 through 219 removed outlier: 3.675A pdb=" N GLY A 216 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 217 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 218 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 219' Processing helix chain 'A' and resid 226 through 246 removed outlier: 3.503A pdb=" N GLU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 276 through 294 removed outlier: 3.576A pdb=" N VAL A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 321 removed outlier: 3.531A pdb=" N ILE A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 321 " --> pdb=" O TYR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.511A pdb=" N VAL A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 408 removed outlier: 4.001A pdb=" N GLY A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 424 Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.620A pdb=" N LYS A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.621A pdb=" N GLN A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 517 removed outlier: 3.708A pdb=" N ILE A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 60 through 73 removed outlier: 3.845A pdb=" N SER B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 75 through 90 Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 98 through 103 removed outlier: 4.432A pdb=" N MET B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 127 Processing helix chain 'B' and resid 128 through 144 removed outlier: 4.084A pdb=" N THR B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 170 Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.807A pdb=" N HIS B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 202 removed outlier: 4.125A pdb=" N SER B 190 " --> pdb=" O PRO B 186 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLN B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 removed outlier: 3.597A pdb=" N LEU B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 219 Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.882A pdb=" N TYR B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 248 removed outlier: 3.721A pdb=" N LEU B 240 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 571 Processing helix chain 'B' and resid 577 through 609 removed outlier: 4.224A pdb=" N ASP B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B 603 " --> pdb=" O TYR B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 635 removed outlier: 3.897A pdb=" N PHE B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE B 631 " --> pdb=" O TYR B 627 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 635 " --> pdb=" O PHE B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 642 removed outlier: 3.801A pdb=" N HIS B 641 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 669 removed outlier: 3.820A pdb=" N LEU B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 703 Processing helix chain 'B' and resid 707 through 723 Processing helix chain 'B' and resid 729 through 737 Processing helix chain 'B' and resid 744 through 766 removed outlier: 3.637A pdb=" N LEU B 748 " --> pdb=" O SER B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 786 through 798 removed outlier: 3.710A pdb=" N HIS B 790 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR B 791 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 795 " --> pdb=" O TYR B 791 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 796 " --> pdb=" O TYR B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 removed outlier: 3.558A pdb=" N GLY B 803 " --> pdb=" O PHE B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 819 removed outlier: 3.688A pdb=" N PHE B 811 " --> pdb=" O ASN B 807 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR B 812 " --> pdb=" O ASP B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 843 removed outlier: 4.142A pdb=" N LYS B 834 " --> pdb=" O PRO B 830 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR B 835 " --> pdb=" O ILE B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 858 through 863 Processing helix chain 'B' and resid 990 through 1002 removed outlier: 3.519A pdb=" N ILE B 994 " --> pdb=" O ASP B 990 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 998 " --> pdb=" O ILE B 994 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1018 removed outlier: 3.866A pdb=" N LEU B1009 " --> pdb=" O ALA B1005 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B1011 " --> pdb=" O HIS B1007 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE B1014 " --> pdb=" O TRP B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1028 Processing helix chain 'B' and resid 1039 through 1047 removed outlier: 4.325A pdb=" N HIS B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N CYS B1045 " --> pdb=" O VAL B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1063 Processing helix chain 'B' and resid 1064 through 1066 No H-bonds generated for 'chain 'B' and resid 1064 through 1066' Processing helix chain 'B' and resid 1067 through 1077 removed outlier: 4.334A pdb=" N LEU B1073 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B1074 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU B1077 " --> pdb=" O LEU B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1108 Processing helix chain 'B' and resid 1210 through 1219 Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 removed outlier: 8.600A pdb=" N LEU A 82 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE A 84 " --> pdb=" O PRO A 38 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE A 40 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ALA A 6 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N CYS A 105 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 8 " --> pdb=" O CYS A 105 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N GLU A 107 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N TRP A 10 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS A 102 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL A 133 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE A 104 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LYS A 135 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE A 106 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 21 removed outlier: 3.736A pdb=" N GLU B 21 " --> pdb=" O THR B 24 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1512 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: 3.17 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3108 1.34 - 1.46: 2250 1.46 - 1.58: 5148 1.58 - 1.70: 4 1.70 - 1.83: 106 Bond restraints: 10616 Sorted by residual: bond pdb=" C4A FAD A 602 " pdb=" C5A FAD A 602 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5X FAD A 602 " pdb=" C9A FAD A 602 " ideal model delta sigma weight residual 1.412 1.492 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C5A FAD A 602 " pdb=" C6A FAD A 602 " ideal model delta sigma weight residual 1.407 1.482 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CA GLN B 573 " pdb=" CB GLN B 573 " ideal model delta sigma weight residual 1.529 1.581 -0.052 1.38e-02 5.25e+03 1.40e+01 bond pdb=" C7 FAD A 602 " pdb=" C8 FAD A 602 " ideal model delta sigma weight residual 1.420 1.488 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 10611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 14062 2.67 - 5.34: 274 5.34 - 8.01: 50 8.01 - 10.69: 15 10.69 - 13.36: 4 Bond angle restraints: 14405 Sorted by residual: angle pdb=" N TRP B 3 " pdb=" CA TRP B 3 " pdb=" C TRP B 3 " ideal model delta sigma weight residual 113.89 103.07 10.82 1.58e+00 4.01e-01 4.69e+01 angle pdb=" N LEU B 998 " pdb=" CA LEU B 998 " pdb=" C LEU B 998 " ideal model delta sigma weight residual 111.36 104.85 6.51 1.09e+00 8.42e-01 3.57e+01 angle pdb=" N LEU B1211 " pdb=" CA LEU B1211 " pdb=" C LEU B1211 " ideal model delta sigma weight residual 111.71 105.25 6.46 1.15e+00 7.56e-01 3.16e+01 angle pdb=" CA LYS B1117 " pdb=" CB LYS B1117 " pdb=" CG LYS B1117 " ideal model delta sigma weight residual 114.10 123.86 -9.76 2.00e+00 2.50e-01 2.38e+01 angle pdb=" CA TRP B1210 " pdb=" CB TRP B1210 " pdb=" CG TRP B1210 " ideal model delta sigma weight residual 113.60 122.15 -8.55 1.90e+00 2.77e-01 2.03e+01 ... (remaining 14400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5403 17.85 - 35.70: 722 35.70 - 53.55: 197 53.55 - 71.40: 37 71.40 - 89.25: 16 Dihedral angle restraints: 6375 sinusoidal: 2648 harmonic: 3727 Sorted by residual: dihedral pdb=" CD ARG B1216 " pdb=" NE ARG B1216 " pdb=" CZ ARG B1216 " pdb=" NH1 ARG B1216 " ideal model delta sinusoidal sigma weight residual 0.00 52.13 -52.13 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CA HIS B1036 " pdb=" C HIS B1036 " pdb=" N ILE B1037 " pdb=" CA ILE B1037 " ideal model delta harmonic sigma weight residual 180.00 -154.22 -25.78 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA MET B1065 " pdb=" C MET B1065 " pdb=" N LEU B1066 " pdb=" CA LEU B1066 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 6372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1371 0.068 - 0.136: 202 0.136 - 0.204: 29 0.204 - 0.273: 2 0.273 - 0.341: 1 Chirality restraints: 1605 Sorted by residual: chirality pdb=" CA MET B1038 " pdb=" N MET B1038 " pdb=" C MET B1038 " pdb=" CB MET B1038 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB THR B 626 " pdb=" CA THR B 626 " pdb=" OG1 THR B 626 " pdb=" CG2 THR B 626 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE B 642 " pdb=" CA ILE B 642 " pdb=" CG1 ILE B 642 " pdb=" CG2 ILE B 642 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1602 not shown) Planarity restraints: 1827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1216 " -0.864 9.50e-02 1.11e+02 3.87e-01 9.11e+01 pdb=" NE ARG B1216 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG B1216 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B1216 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B1216 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1210 " 0.031 2.00e-02 2.50e+03 1.90e-02 9.00e+00 pdb=" CG TRP B1210 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B1210 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B1210 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1210 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B1210 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B1210 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1210 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1210 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B1210 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 850 " 0.018 2.00e-02 2.50e+03 1.80e-02 8.12e+00 pdb=" CG TRP B 850 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 850 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 850 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 850 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 850 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 850 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 850 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 850 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 850 " 0.002 2.00e-02 2.50e+03 ... (remaining 1824 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2731 2.80 - 3.32: 10040 3.32 - 3.85: 17587 3.85 - 4.37: 20295 4.37 - 4.90: 33540 Nonbonded interactions: 84193 Sorted by model distance: nonbonded pdb=" OG1 THR B 577 " pdb=" OD1 ASP B 579 " model vdw 2.272 3.040 nonbonded pdb=" O LEU B 209 " pdb=" OG1 THR B 213 " model vdw 2.275 3.040 nonbonded pdb=" O SER B 777 " pdb=" OG1 THR B 781 " model vdw 2.283 3.040 nonbonded pdb=" ND2 ASN B 701 " pdb=" OE1 GLN B 718 " model vdw 2.296 3.120 nonbonded pdb=" O SER B1130 " pdb=" OG SER B1130 " model vdw 2.296 3.040 ... (remaining 84188 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.800 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 0.005 0.085 10616 Z= 0.309 Angle : 0.944 13.358 14405 Z= 0.513 Chirality : 0.051 0.341 1605 Planarity : 0.011 0.387 1827 Dihedral : 17.626 89.249 3959 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.44 % Allowed : 24.80 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.22), residues: 1263 helix: -1.53 (0.16), residues: 749 sheet: -0.48 (1.04), residues: 35 loop : -1.65 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B1210 HIS 0.006 0.001 HIS B1075 PHE 0.034 0.002 PHE B 811 TYR 0.020 0.001 TYR B1095 ARG 0.006 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8624 (tp) cc_final: 0.8385 (tp) REVERT: A 270 LEU cc_start: 0.8667 (tt) cc_final: 0.8182 (mp) REVERT: B 179 MET cc_start: 0.4316 (ptt) cc_final: 0.4073 (ptt) REVERT: B 185 MET cc_start: 0.6852 (mmm) cc_final: 0.6359 (mmm) REVERT: B 191 MET cc_start: 0.6944 (ttm) cc_final: 0.6744 (ttp) REVERT: B 211 LEU cc_start: 0.8697 (tp) cc_final: 0.8380 (mt) REVERT: B 789 MET cc_start: 0.5516 (mmt) cc_final: 0.4916 (mmm) REVERT: B 813 MET cc_start: 0.6151 (tmm) cc_final: 0.5627 (tmm) REVERT: B 814 MET cc_start: 0.7873 (mmt) cc_final: 0.7371 (mmp) REVERT: B 1075 HIS cc_start: 0.8218 (p90) cc_final: 0.7940 (p-80) outliers start: 5 outliers final: 0 residues processed: 112 average time/residue: 0.2306 time to fit residues: 37.2552 Evaluate side-chains 92 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 HIS B1036 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10616 Z= 0.206 Angle : 0.645 7.866 14405 Z= 0.328 Chirality : 0.042 0.161 1605 Planarity : 0.005 0.051 1827 Dihedral : 6.625 75.660 1426 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.71 % Allowed : 22.18 % Favored : 75.11 % 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 (0.24), residues: 1263 helix: -0.16 (0.18), residues: 757 sheet: -0.27 (1.12), residues: 35 loop : -1.45 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1210 HIS 0.005 0.001 HIS B1075 PHE 0.029 0.002 PHE B 811 TYR 0.019 0.001 TYR B1043 ARG 0.003 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8072 (tpp-160) REVERT: A 90 TYR cc_start: 0.8555 (t80) cc_final: 0.8354 (t80) REVERT: A 410 ASP cc_start: 0.8395 (p0) cc_final: 0.8011 (p0) REVERT: B 191 MET cc_start: 0.7213 (ttm) cc_final: 0.6790 (ttp) REVERT: B 724 MET cc_start: 0.6779 (tpp) cc_final: 0.6435 (tpp) REVERT: B 814 MET cc_start: 0.7983 (mmt) cc_final: 0.7631 (mmp) REVERT: B 1038 MET cc_start: 0.5577 (ttm) cc_final: 0.4995 (tpt) outliers start: 31 outliers final: 11 residues processed: 121 average time/residue: 0.2252 time to fit residues: 39.5148 Evaluate side-chains 91 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 1073 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 123 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN A 285 HIS ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10616 Z= 0.299 Angle : 0.647 7.740 14405 Z= 0.329 Chirality : 0.043 0.231 1605 Planarity : 0.005 0.054 1827 Dihedral : 6.568 75.933 1426 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.58 % Allowed : 22.88 % Favored : 73.54 % 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: -0.57 (0.24), residues: 1263 helix: 0.23 (0.19), residues: 772 sheet: -0.64 (1.07), residues: 35 loop : -1.29 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1210 HIS 0.005 0.001 HIS B1075 PHE 0.034 0.002 PHE B 811 TYR 0.021 0.002 TYR B 597 ARG 0.004 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 1.085 Fit side-chains REVERT: A 58 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8046 (tpp-160) REVERT: B 191 MET cc_start: 0.7263 (ttm) cc_final: 0.6800 (ttp) REVERT: B 724 MET cc_start: 0.7589 (tpp) cc_final: 0.7251 (tpp) REVERT: B 734 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6713 (mm) REVERT: B 850 TRP cc_start: 0.5691 (p90) cc_final: 0.5262 (m-90) REVERT: B 1102 TYR cc_start: 0.4773 (OUTLIER) cc_final: 0.4216 (p90) outliers start: 41 outliers final: 21 residues processed: 116 average time/residue: 0.2335 time to fit residues: 38.9474 Evaluate side-chains 98 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1102 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10616 Z= 0.231 Angle : 0.593 8.138 14405 Z= 0.302 Chirality : 0.042 0.244 1605 Planarity : 0.004 0.057 1827 Dihedral : 6.323 77.925 1426 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.67 % Allowed : 23.32 % Favored : 73.01 % 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: -0.27 (0.25), residues: 1263 helix: 0.49 (0.19), residues: 770 sheet: -0.76 (1.04), residues: 35 loop : -1.19 (0.32), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 623 HIS 0.003 0.001 HIS B1075 PHE 0.031 0.001 PHE B 811 TYR 0.020 0.002 TYR B 597 ARG 0.003 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 78 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8055 (tpp-160) REVERT: A 357 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: A 410 ASP cc_start: 0.8452 (p0) cc_final: 0.8033 (p0) REVERT: B 191 MET cc_start: 0.7378 (ttm) cc_final: 0.6993 (ttp) REVERT: B 724 MET cc_start: 0.7602 (tpp) cc_final: 0.7191 (tpp) REVERT: B 734 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6908 (mm) REVERT: B 789 MET cc_start: 0.6432 (mmt) cc_final: 0.5544 (mmm) REVERT: B 814 MET cc_start: 0.7764 (mmp) cc_final: 0.7486 (mmp) REVERT: B 850 TRP cc_start: 0.5802 (p90) cc_final: 0.5390 (m-90) REVERT: B 1102 TYR cc_start: 0.4850 (OUTLIER) cc_final: 0.4255 (p90) outliers start: 42 outliers final: 26 residues processed: 117 average time/residue: 0.2529 time to fit residues: 42.9531 Evaluate side-chains 105 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1039 GLU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1102 TYR Chi-restraints excluded: chain B residue 1118 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 713 HIS B 782 GLN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10616 Z= 0.356 Angle : 0.659 8.880 14405 Z= 0.332 Chirality : 0.045 0.305 1605 Planarity : 0.005 0.049 1827 Dihedral : 6.362 87.014 1426 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.15 % Allowed : 22.18 % Favored : 72.66 % 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: -0.38 (0.24), residues: 1263 helix: 0.40 (0.19), residues: 772 sheet: -1.21 (0.98), residues: 35 loop : -1.20 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 850 HIS 0.004 0.001 HIS B1075 PHE 0.031 0.002 PHE B 811 TYR 0.026 0.002 TYR B 597 ARG 0.004 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 79 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8029 (tpp-160) REVERT: B 724 MET cc_start: 0.7820 (tpp) cc_final: 0.7468 (tpp) REVERT: B 734 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6921 (mm) REVERT: B 789 MET cc_start: 0.6543 (mmt) cc_final: 0.5555 (mmm) REVERT: B 814 MET cc_start: 0.7805 (mmp) cc_final: 0.7448 (mmp) REVERT: B 850 TRP cc_start: 0.5681 (p90) cc_final: 0.5032 (m-90) REVERT: B 1075 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.8055 (p-80) REVERT: B 1096 TRP cc_start: 0.6714 (m-10) cc_final: 0.6508 (m100) REVERT: B 1102 TYR cc_start: 0.4991 (OUTLIER) cc_final: 0.4335 (p90) outliers start: 59 outliers final: 34 residues processed: 132 average time/residue: 0.2174 time to fit residues: 41.9165 Evaluate side-chains 113 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 75 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1039 GLU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1075 HIS Chi-restraints excluded: chain B residue 1102 TYR Chi-restraints excluded: chain B residue 1118 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.5980 chunk 109 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 701 ASN B 718 GLN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10616 Z= 0.194 Angle : 0.600 15.675 14405 Z= 0.299 Chirality : 0.042 0.265 1605 Planarity : 0.004 0.065 1827 Dihedral : 6.123 88.742 1426 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.10 % Allowed : 23.06 % Favored : 72.84 % 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: -0.10 (0.24), residues: 1263 helix: 0.65 (0.19), residues: 768 sheet: -1.16 (0.98), residues: 35 loop : -1.11 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 850 HIS 0.003 0.000 HIS B 815 PHE 0.023 0.001 PHE B 811 TYR 0.019 0.002 TYR B1067 ARG 0.002 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 79 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8229 (mp) REVERT: A 58 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8036 (tpp-160) REVERT: A 357 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: A 410 ASP cc_start: 0.8458 (p0) cc_final: 0.8018 (p0) REVERT: B 724 MET cc_start: 0.7615 (tpp) cc_final: 0.7308 (tpp) REVERT: B 734 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6879 (mm) REVERT: B 789 MET cc_start: 0.6396 (mmt) cc_final: 0.5815 (mmm) REVERT: B 813 MET cc_start: 0.6431 (tpp) cc_final: 0.5945 (ttt) REVERT: B 850 TRP cc_start: 0.5719 (p90) cc_final: 0.4948 (m-90) REVERT: B 1102 TYR cc_start: 0.5015 (OUTLIER) cc_final: 0.4345 (p90) outliers start: 47 outliers final: 30 residues processed: 122 average time/residue: 0.2372 time to fit residues: 42.2354 Evaluate side-chains 111 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1039 GLU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1075 HIS Chi-restraints excluded: chain B residue 1102 TYR Chi-restraints excluded: chain B residue 1118 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 76 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.0270 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 782 GLN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10616 Z= 0.181 Angle : 0.589 12.748 14405 Z= 0.294 Chirality : 0.041 0.247 1605 Planarity : 0.004 0.061 1827 Dihedral : 5.956 87.437 1426 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.58 % Allowed : 23.32 % Favored : 73.10 % 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: 0.04 (0.25), residues: 1263 helix: 0.76 (0.19), residues: 767 sheet: -1.10 (0.98), residues: 35 loop : -1.06 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1096 HIS 0.005 0.000 HIS B 605 PHE 0.030 0.001 PHE B 811 TYR 0.016 0.001 TYR B1095 ARG 0.002 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8023 (tpp-160) REVERT: A 357 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: A 410 ASP cc_start: 0.8321 (p0) cc_final: 0.7935 (p0) REVERT: B 724 MET cc_start: 0.7520 (tpp) cc_final: 0.7200 (tpp) REVERT: B 789 MET cc_start: 0.6320 (mmt) cc_final: 0.5908 (mmm) REVERT: B 813 MET cc_start: 0.6758 (tpp) cc_final: 0.6407 (ttt) REVERT: B 850 TRP cc_start: 0.5880 (p90) cc_final: 0.5075 (m-90) REVERT: B 1102 TYR cc_start: 0.4995 (OUTLIER) cc_final: 0.4343 (p90) outliers start: 41 outliers final: 31 residues processed: 117 average time/residue: 0.2398 time to fit residues: 40.2389 Evaluate side-chains 111 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1039 GLU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1075 HIS Chi-restraints excluded: chain B residue 1102 TYR Chi-restraints excluded: chain B residue 1118 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 0.0010 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10616 Z= 0.226 Angle : 0.602 11.746 14405 Z= 0.301 Chirality : 0.042 0.224 1605 Planarity : 0.004 0.058 1827 Dihedral : 5.922 88.610 1426 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.49 % Allowed : 24.19 % Favored : 72.31 % 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: 0.03 (0.25), residues: 1263 helix: 0.74 (0.19), residues: 771 sheet: -1.13 (0.98), residues: 35 loop : -1.04 (0.32), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B1096 HIS 0.004 0.001 HIS B 574 PHE 0.032 0.001 PHE B 811 TYR 0.017 0.001 TYR B1095 ARG 0.002 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8042 (tpp-160) REVERT: A 357 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: A 410 ASP cc_start: 0.8412 (p0) cc_final: 0.8050 (p0) REVERT: B 191 MET cc_start: 0.7650 (ttm) cc_final: 0.6978 (ttp) REVERT: B 724 MET cc_start: 0.7574 (tpp) cc_final: 0.7252 (tpp) REVERT: B 789 MET cc_start: 0.6490 (mmt) cc_final: 0.6114 (mmm) REVERT: B 813 MET cc_start: 0.6747 (tpp) cc_final: 0.6436 (ttt) REVERT: B 850 TRP cc_start: 0.5948 (p90) cc_final: 0.5066 (m-90) REVERT: B 1102 TYR cc_start: 0.5010 (OUTLIER) cc_final: 0.4376 (p90) outliers start: 40 outliers final: 33 residues processed: 113 average time/residue: 0.2409 time to fit residues: 39.5440 Evaluate side-chains 114 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1039 GLU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1075 HIS Chi-restraints excluded: chain B residue 1102 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 0.0030 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 112 optimal weight: 0.0270 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 0.0670 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS B 226 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10616 Z= 0.161 Angle : 0.589 11.702 14405 Z= 0.291 Chirality : 0.040 0.179 1605 Planarity : 0.004 0.057 1827 Dihedral : 5.781 86.518 1426 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.88 % Allowed : 24.54 % Favored : 72.58 % 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: 0.19 (0.25), residues: 1263 helix: 0.83 (0.19), residues: 780 sheet: -0.99 (0.99), residues: 35 loop : -0.94 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B1096 HIS 0.004 0.000 HIS B 574 PHE 0.028 0.001 PHE B 811 TYR 0.012 0.001 TYR B1095 ARG 0.002 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8469 (tt) cc_final: 0.8119 (mp) REVERT: A 357 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: B 191 MET cc_start: 0.7555 (ttm) cc_final: 0.7178 (ttp) REVERT: B 724 MET cc_start: 0.7478 (tpp) cc_final: 0.7169 (tpp) REVERT: B 789 MET cc_start: 0.6504 (mmt) cc_final: 0.6175 (mmm) REVERT: B 813 MET cc_start: 0.6835 (tpp) cc_final: 0.6452 (ttt) REVERT: B 850 TRP cc_start: 0.5827 (p90) cc_final: 0.4870 (m-90) REVERT: B 1038 MET cc_start: 0.6497 (tpp) cc_final: 0.6099 (tpp) REVERT: B 1075 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.8116 (p-80) REVERT: B 1102 TYR cc_start: 0.4802 (OUTLIER) cc_final: 0.4187 (p90) outliers start: 33 outliers final: 23 residues processed: 108 average time/residue: 0.2301 time to fit residues: 36.9014 Evaluate side-chains 103 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1039 GLU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1075 HIS Chi-restraints excluded: chain B residue 1102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.0070 chunk 61 optimal weight: 0.0030 chunk 79 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.1812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 701 ASN B 718 GLN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10616 Z= 0.258 Angle : 0.633 11.106 14405 Z= 0.312 Chirality : 0.042 0.211 1605 Planarity : 0.004 0.056 1827 Dihedral : 5.858 89.691 1426 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.62 % Allowed : 25.24 % Favored : 72.14 % 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: 0.13 (0.25), residues: 1263 helix: 0.79 (0.19), residues: 775 sheet: -1.06 (0.97), residues: 35 loop : -0.98 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B1096 HIS 0.007 0.001 HIS A 285 PHE 0.028 0.001 PHE B 811 TYR 0.016 0.001 TYR B 597 ARG 0.005 0.000 ARG A 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8145 (mt0) cc_final: 0.7855 (mp10) REVERT: A 58 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8028 (tpp-160) REVERT: A 357 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8417 (mm-40) REVERT: B 191 MET cc_start: 0.7663 (ttm) cc_final: 0.7007 (ttp) REVERT: B 568 MET cc_start: 0.5300 (mtt) cc_final: 0.5096 (mmm) REVERT: B 724 MET cc_start: 0.7560 (tpp) cc_final: 0.7243 (tpp) REVERT: B 813 MET cc_start: 0.6880 (tpp) cc_final: 0.6500 (ttt) REVERT: B 850 TRP cc_start: 0.5829 (p90) cc_final: 0.4848 (m-90) REVERT: B 1038 MET cc_start: 0.6711 (tpp) cc_final: 0.6187 (tpt) REVERT: B 1102 TYR cc_start: 0.5046 (OUTLIER) cc_final: 0.4436 (p90) outliers start: 30 outliers final: 23 residues processed: 104 average time/residue: 0.2416 time to fit residues: 36.2951 Evaluate side-chains 105 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1039 GLU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1075 HIS Chi-restraints excluded: chain B residue 1102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 14 optimal weight: 0.0770 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS ** B 816 HIS ** 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 = 0.4049 r_free = 0.4049 target = 0.119681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.080884 restraints weight = 24948.517| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.84 r_work: 0.3163 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10616 Z= 0.193 Angle : 0.606 11.662 14405 Z= 0.298 Chirality : 0.041 0.183 1605 Planarity : 0.004 0.055 1827 Dihedral : 5.814 89.961 1426 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.45 % Allowed : 24.72 % Favored : 72.84 % 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: 0.22 (0.25), residues: 1263 helix: 0.87 (0.19), residues: 775 sheet: -1.04 (0.97), residues: 35 loop : -0.94 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B1096 HIS 0.004 0.001 HIS B 574 PHE 0.027 0.001 PHE B 811 TYR 0.015 0.001 TYR B 792 ARG 0.002 0.000 ARG A 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.71 seconds wall clock time: 40 minutes 29.73 seconds (2429.73 seconds total)