Starting phenix.real_space_refine on Mon Jul 28 19:33:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dd7_27335/07_2025/8dd7_27335.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dd7_27335/07_2025/8dd7_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_27335/07_2025/8dd7_27335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dd7_27335/07_2025/8dd7_27335.map" model { file = "/net/cci-nas-00/data/ceres_data/8dd7_27335/07_2025/8dd7_27335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dd7_27335/07_2025/8dd7_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-5711/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: 6.60, per 1000 atoms: 0.64 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: 2.81 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: 0.96 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: 3.01 Time building geometry restraints manager: 3.13 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: 2.530 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.190 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.190 ------------------------------------------------------------------------------- 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= 0.263 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 Details of bonding type rmsd hydrogen bonds : bond 0.22333 ( 516) hydrogen bonds : angle 7.75510 ( 1512) covalent geometry : bond 0.00484 (10616) covalent geometry : angle 0.94380 (14405) *********************** 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 : 1.287 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: 0.2335 time to fit residues: 37.8221 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 : 1.290 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.124199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086006 restraints weight = 25158.939| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.94 r_work: 0.3263 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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= 0.148 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 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 516) hydrogen bonds : angle 5.02536 ( 1512) covalent geometry : bond 0.00317 (10616) covalent geometry : angle 0.64461 (14405) *********************** 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 : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8571 (tpp-160) REVERT: A 410 ASP cc_start: 0.8619 (p0) cc_final: 0.8303 (p0) REVERT: B 179 MET cc_start: 0.4663 (ptt) cc_final: 0.4422 (ptt) REVERT: B 191 MET cc_start: 0.7249 (ttm) cc_final: 0.6818 (ttp) REVERT: B 724 MET cc_start: 0.7005 (tpp) cc_final: 0.6641 (tpp) REVERT: B 814 MET cc_start: 0.7993 (mmt) cc_final: 0.7615 (mmp) REVERT: B 1038 MET cc_start: 0.5533 (ttm) cc_final: 0.4876 (tpt) outliers start: 31 outliers final: 11 residues processed: 121 average time/residue: 0.2320 time to fit residues: 40.8920 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 : 1.175 ------------------------------------------------------------------------------- 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 36 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.119448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082688 restraints weight = 25434.235| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.60 r_work: 0.3137 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10616 Z= 0.206 Angle : 0.654 7.358 14405 Z= 0.333 Chirality : 0.044 0.240 1605 Planarity : 0.005 0.051 1827 Dihedral : 6.594 75.649 1426 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.49 % Allowed : 22.79 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1263 helix: 0.24 (0.19), residues: 770 sheet: -0.68 (1.07), residues: 35 loop : -1.27 (0.31), residues: 458 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 0.022 0.002 TYR A 90 ARG 0.005 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 516) hydrogen bonds : angle 4.78991 ( 1512) covalent geometry : bond 0.00468 (10616) covalent geometry : angle 0.65419 (14405) *********************** 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 117 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 1.151 Fit side-chains REVERT: A 58 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8593 (tpp-160) REVERT: B 191 MET cc_start: 0.7417 (ttm) cc_final: 0.6941 (ttp) REVERT: B 724 MET cc_start: 0.7794 (tpp) cc_final: 0.7504 (tpp) REVERT: B 734 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6823 (mm) REVERT: B 850 TRP cc_start: 0.5811 (p90) cc_final: 0.5389 (m-90) REVERT: B 1102 TYR cc_start: 0.4823 (OUTLIER) cc_final: 0.4262 (p90) outliers start: 40 outliers final: 19 residues processed: 114 average time/residue: 0.2258 time to fit residues: 37.2781 Evaluate side-chains 95 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 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 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 14 optimal weight: 0.7980 chunk 65 optimal weight: 0.0980 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.121131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085144 restraints weight = 25273.224| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.70 r_work: 0.3147 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10616 Z= 0.164 Angle : 0.596 7.939 14405 Z= 0.304 Chirality : 0.042 0.264 1605 Planarity : 0.004 0.054 1827 Dihedral : 6.376 77.210 1426 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.58 % Allowed : 23.84 % 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: -0.31 (0.24), residues: 1263 helix: 0.46 (0.19), residues: 770 sheet: -0.80 (1.04), residues: 35 loop : -1.21 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 850 HIS 0.003 0.001 HIS B1075 PHE 0.035 0.002 PHE B 811 TYR 0.020 0.002 TYR B 597 ARG 0.003 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 516) hydrogen bonds : angle 4.65739 ( 1512) covalent geometry : bond 0.00375 (10616) covalent geometry : angle 0.59642 (14405) *********************** 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: 41 poor density : 79 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8574 (tpp-160) REVERT: A 357 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: A 410 ASP cc_start: 0.8739 (p0) cc_final: 0.8496 (p0) REVERT: B 191 MET cc_start: 0.7583 (ttm) cc_final: 0.7184 (ttp) REVERT: B 714 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7854 (mp) REVERT: B 724 MET cc_start: 0.7777 (tpp) cc_final: 0.7376 (tpp) REVERT: B 734 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6979 (mm) REVERT: B 789 MET cc_start: 0.6539 (mmt) cc_final: 0.5903 (mmm) REVERT: B 813 MET cc_start: 0.7005 (tpp) cc_final: 0.6402 (ttt) REVERT: B 814 MET cc_start: 0.7894 (mmp) cc_final: 0.7592 (mmp) REVERT: B 850 TRP cc_start: 0.5802 (p90) cc_final: 0.5426 (m-90) REVERT: B 1102 TYR cc_start: 0.4842 (OUTLIER) cc_final: 0.4249 (p90) outliers start: 41 outliers final: 26 residues processed: 117 average time/residue: 0.2325 time to fit residues: 39.7595 Evaluate side-chains 104 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 167 ILE 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 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 714 LEU 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 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.121101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.085697 restraints weight = 24940.498| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 4.08 r_work: 0.3180 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10616 Z= 0.123 Angle : 0.568 8.522 14405 Z= 0.286 Chirality : 0.041 0.209 1605 Planarity : 0.004 0.048 1827 Dihedral : 6.077 81.659 1426 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.93 % Allowed : 23.32 % Favored : 72.75 % 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: 0.73 (0.19), residues: 759 sheet: -0.79 (1.03), residues: 35 loop : -1.14 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1096 HIS 0.005 0.001 HIS B 815 PHE 0.027 0.001 PHE B 811 TYR 0.015 0.001 TYR B 597 ARG 0.004 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 516) hydrogen bonds : angle 4.48533 ( 1512) covalent geometry : bond 0.00274 (10616) covalent geometry : angle 0.56796 (14405) *********************** 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 126 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 81 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.8137 (mmt) cc_final: 0.7437 (mmt) REVERT: A 270 LEU cc_start: 0.8744 (tt) cc_final: 0.8450 (mp) REVERT: A 357 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8148 (mp10) REVERT: A 410 ASP cc_start: 0.8636 (p0) cc_final: 0.8383 (p0) REVERT: B 102 MET cc_start: 0.8074 (ppp) cc_final: 0.7840 (ppp) REVERT: B 191 MET cc_start: 0.7582 (ttm) cc_final: 0.7167 (ttp) REVERT: B 724 MET cc_start: 0.7772 (tpp) cc_final: 0.7346 (tpp) REVERT: B 789 MET cc_start: 0.6430 (mmt) cc_final: 0.5523 (mmm) REVERT: B 813 MET cc_start: 0.6820 (tpp) cc_final: 0.6304 (ttt) REVERT: B 814 MET cc_start: 0.7887 (mmp) cc_final: 0.7563 (mmp) REVERT: B 850 TRP cc_start: 0.5773 (p90) cc_final: 0.5158 (m-90) REVERT: B 1102 TYR cc_start: 0.4806 (OUTLIER) cc_final: 0.4173 (p90) outliers start: 45 outliers final: 27 residues processed: 120 average time/residue: 0.2134 time to fit residues: 37.8587 Evaluate side-chains 105 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 218 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.0470 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 108 optimal weight: 0.0470 chunk 85 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.121293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086244 restraints weight = 25114.645| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.03 r_work: 0.3189 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10616 Z= 0.120 Angle : 0.581 16.781 14405 Z= 0.287 Chirality : 0.041 0.192 1605 Planarity : 0.004 0.059 1827 Dihedral : 5.880 83.530 1426 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.10 % Allowed : 22.62 % Favored : 73.28 % 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: 0.82 (0.19), residues: 767 sheet: -0.71 (1.03), residues: 35 loop : -1.03 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1096 HIS 0.003 0.000 HIS B 574 PHE 0.022 0.001 PHE B 811 TYR 0.018 0.001 TYR B1095 ARG 0.002 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 516) hydrogen bonds : angle 4.40541 ( 1512) covalent geometry : bond 0.00267 (10616) covalent geometry : angle 0.58100 (14405) *********************** 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 125 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 78 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.8055 (mmt) cc_final: 0.7323 (mmt) REVERT: A 270 LEU cc_start: 0.8708 (tt) cc_final: 0.8478 (mp) REVERT: A 357 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: A 410 ASP cc_start: 0.8599 (p0) cc_final: 0.8273 (p0) REVERT: B 102 MET cc_start: 0.8008 (ppp) cc_final: 0.7751 (ppp) REVERT: B 191 MET cc_start: 0.7561 (ttm) cc_final: 0.7141 (ttp) REVERT: B 649 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8576 (t0) REVERT: B 714 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7864 (mp) REVERT: B 724 MET cc_start: 0.7751 (tpp) cc_final: 0.7331 (tpp) REVERT: B 789 MET cc_start: 0.6430 (mmt) cc_final: 0.5903 (mmm) REVERT: B 814 MET cc_start: 0.7888 (mmp) cc_final: 0.7674 (mmp) REVERT: B 850 TRP cc_start: 0.5843 (p90) cc_final: 0.5165 (m-90) REVERT: B 1038 MET cc_start: 0.6679 (ttm) cc_final: 0.6201 (tpt) REVERT: B 1101 MET cc_start: 0.7203 (mtt) cc_final: 0.6952 (mtt) REVERT: B 1102 TYR cc_start: 0.4808 (OUTLIER) cc_final: 0.4229 (p90) outliers start: 47 outliers final: 31 residues processed: 121 average time/residue: 0.2249 time to fit residues: 40.6376 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 : 1.210 ------------------------------------------------------------------------------- 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 52 VAL 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 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 32 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 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 733 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 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 37 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 108 optimal weight: 0.0070 chunk 59 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.120133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081791 restraints weight = 25306.109| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.92 r_work: 0.3175 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10616 Z= 0.125 Angle : 0.573 11.659 14405 Z= 0.285 Chirality : 0.041 0.177 1605 Planarity : 0.004 0.057 1827 Dihedral : 5.817 85.192 1426 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.02 % Allowed : 22.45 % 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: 0.21 (0.25), residues: 1263 helix: 0.89 (0.19), residues: 767 sheet: -0.75 (1.02), residues: 35 loop : -1.00 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B1096 HIS 0.004 0.000 HIS B 574 PHE 0.020 0.001 PHE B 811 TYR 0.019 0.001 TYR B1095 ARG 0.002 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 516) hydrogen bonds : angle 4.35396 ( 1512) covalent geometry : bond 0.00286 (10616) covalent geometry : angle 0.57345 (14405) *********************** 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 123 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 77 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8512 (tpp-160) REVERT: A 266 MET cc_start: 0.8064 (mmt) cc_final: 0.7359 (mmt) REVERT: A 270 LEU cc_start: 0.8676 (tt) cc_final: 0.8400 (mp) REVERT: A 357 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8167 (mp10) REVERT: A 410 ASP cc_start: 0.8613 (p0) cc_final: 0.8305 (p0) REVERT: B 191 MET cc_start: 0.7571 (ttm) cc_final: 0.7157 (ttp) REVERT: B 724 MET cc_start: 0.7813 (tpp) cc_final: 0.7404 (tpp) REVERT: B 789 MET cc_start: 0.6549 (mmt) cc_final: 0.6046 (mmm) REVERT: B 814 MET cc_start: 0.7842 (mmp) cc_final: 0.7628 (mmp) REVERT: B 850 TRP cc_start: 0.5912 (p90) cc_final: 0.5151 (m-90) REVERT: B 1038 MET cc_start: 0.6727 (ttm) cc_final: 0.6422 (tpt) REVERT: B 1039 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6881 (tp30) REVERT: B 1102 TYR cc_start: 0.4898 (OUTLIER) cc_final: 0.4275 (p90) outliers start: 46 outliers final: 33 residues processed: 119 average time/residue: 0.2169 time to fit residues: 38.5154 Evaluate side-chains 110 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 285 HIS 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 32 LEU Chi-restraints excluded: chain B residue 51 THR 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 709 ASP Chi-restraints excluded: chain B residue 723 GLU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 113 optimal weight: 0.3980 chunk 102 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 713 HIS B 816 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.120059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081619 restraints weight = 25118.157| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.88 r_work: 0.3174 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10616 Z= 0.130 Angle : 0.581 11.093 14405 Z= 0.288 Chirality : 0.041 0.170 1605 Planarity : 0.004 0.055 1827 Dihedral : 5.776 86.472 1426 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.76 % Allowed : 22.79 % Favored : 73.45 % 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: 0.90 (0.19), residues: 766 sheet: -0.79 (1.02), residues: 35 loop : -0.98 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B1096 HIS 0.017 0.001 HIS A 285 PHE 0.019 0.001 PHE B 811 TYR 0.015 0.001 TYR A 281 ARG 0.003 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 516) hydrogen bonds : angle 4.34688 ( 1512) covalent geometry : bond 0.00296 (10616) covalent geometry : angle 0.58111 (14405) *********************** 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 119 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 76 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8507 (tpp-160) REVERT: A 266 MET cc_start: 0.8042 (mmt) cc_final: 0.7336 (mmt) REVERT: A 270 LEU cc_start: 0.8667 (tt) cc_final: 0.8375 (mp) REVERT: A 357 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: A 410 ASP cc_start: 0.8617 (p0) cc_final: 0.8409 (p0) REVERT: B 191 MET cc_start: 0.7630 (ttm) cc_final: 0.7234 (ttp) REVERT: B 568 MET cc_start: 0.5938 (mpp) cc_final: 0.5114 (mtt) REVERT: B 724 MET cc_start: 0.7808 (tpp) cc_final: 0.7411 (tpp) REVERT: B 789 MET cc_start: 0.6558 (mmt) cc_final: 0.6060 (mmm) REVERT: B 850 TRP cc_start: 0.5957 (p90) cc_final: 0.5097 (m-90) REVERT: B 1038 MET cc_start: 0.6906 (ttm) cc_final: 0.6545 (tpt) REVERT: B 1039 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: B 1102 TYR cc_start: 0.4869 (OUTLIER) cc_final: 0.4261 (p90) outliers start: 43 outliers final: 35 residues processed: 114 average time/residue: 0.2168 time to fit residues: 36.6501 Evaluate side-chains 114 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain A residue 167 ILE 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 32 LEU Chi-restraints excluded: chain B residue 51 THR 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 709 ASP Chi-restraints excluded: chain B residue 723 GLU 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 1088 ILE Chi-restraints excluded: chain B residue 1102 TYR Chi-restraints excluded: chain B residue 1118 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 117 optimal weight: 0.6980 chunk 24 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.117970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.078894 restraints weight = 25357.307| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.92 r_work: 0.3113 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10616 Z= 0.204 Angle : 0.641 11.078 14405 Z= 0.318 Chirality : 0.043 0.177 1605 Planarity : 0.004 0.052 1827 Dihedral : 5.919 88.248 1426 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.41 % Allowed : 23.14 % Favored : 73.45 % 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: 0.06 (0.25), residues: 1263 helix: 0.74 (0.19), residues: 769 sheet: -0.96 (0.99), residues: 35 loop : -0.98 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B1096 HIS 0.004 0.001 HIS B 816 PHE 0.023 0.002 PHE B 811 TYR 0.020 0.002 TYR B 597 ARG 0.003 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 516) hydrogen bonds : angle 4.47683 ( 1512) covalent geometry : bond 0.00476 (10616) covalent geometry : angle 0.64131 (14405) *********************** 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: 39 poor density : 75 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8242 (mt0) cc_final: 0.7935 (mp10) REVERT: A 58 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8532 (tpp-160) REVERT: A 506 MET cc_start: 0.9033 (mmt) cc_final: 0.8826 (mmt) REVERT: B 182 MET cc_start: 0.6716 (tpt) cc_final: 0.6507 (pmm) REVERT: B 191 MET cc_start: 0.7756 (ttm) cc_final: 0.7061 (ttp) REVERT: B 639 MET cc_start: 0.8284 (tpt) cc_final: 0.7995 (tpp) REVERT: B 724 MET cc_start: 0.7944 (tpp) cc_final: 0.7599 (tpp) REVERT: B 813 MET cc_start: 0.6430 (tpp) cc_final: 0.5986 (ttt) REVERT: B 850 TRP cc_start: 0.5943 (p90) cc_final: 0.5005 (m-90) REVERT: B 1038 MET cc_start: 0.7181 (ttm) cc_final: 0.6732 (tpt) REVERT: B 1039 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6990 (tp30) REVERT: B 1102 TYR cc_start: 0.4934 (OUTLIER) cc_final: 0.4349 (p90) outliers start: 39 outliers final: 30 residues processed: 109 average time/residue: 0.2341 time to fit residues: 36.6333 Evaluate side-chains 107 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 162 LEU 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 376 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 51 THR 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 239 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 733 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 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 Chi-restraints excluded: chain B residue 1118 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.119119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.080315 restraints weight = 25141.582| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.89 r_work: 0.3145 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10616 Z= 0.143 Angle : 0.612 11.117 14405 Z= 0.299 Chirality : 0.041 0.172 1605 Planarity : 0.004 0.052 1827 Dihedral : 5.848 89.491 1426 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.06 % Allowed : 23.41 % 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: 0.16 (0.25), residues: 1263 helix: 0.77 (0.19), residues: 781 sheet: -0.96 (0.99), residues: 35 loop : -0.89 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B1096 HIS 0.004 0.001 HIS B 574 PHE 0.016 0.001 PHE B 811 TYR 0.017 0.001 TYR B 597 ARG 0.002 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 516) hydrogen bonds : angle 4.40602 ( 1512) covalent geometry : bond 0.00330 (10616) covalent geometry : angle 0.61237 (14405) ********************** 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 113 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8545 (tpp-160) REVERT: A 410 ASP cc_start: 0.8700 (p0) cc_final: 0.8360 (p0) REVERT: B 568 MET cc_start: 0.5468 (mpp) cc_final: 0.4695 (mtt) REVERT: B 724 MET cc_start: 0.7909 (tpp) cc_final: 0.7559 (tpp) REVERT: B 813 MET cc_start: 0.6626 (tpp) cc_final: 0.6227 (ttt) REVERT: B 814 MET cc_start: 0.7732 (mmp) cc_final: 0.7471 (mmp) REVERT: B 850 TRP cc_start: 0.5972 (p90) cc_final: 0.5022 (m-90) REVERT: B 1017 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7444 (tm-30) REVERT: B 1038 MET cc_start: 0.7135 (ttm) cc_final: 0.6735 (tpt) REVERT: B 1102 TYR cc_start: 0.5053 (OUTLIER) cc_final: 0.4438 (p90) outliers start: 35 outliers final: 30 residues processed: 107 average time/residue: 0.2438 time to fit residues: 37.3744 Evaluate side-chains 107 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 162 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 376 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 51 THR 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 239 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 723 GLU 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 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 49 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.118765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.079797 restraints weight = 24999.176| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.84 r_work: 0.3137 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10616 Z= 0.159 Angle : 0.619 11.662 14405 Z= 0.302 Chirality : 0.042 0.173 1605 Planarity : 0.004 0.051 1827 Dihedral : 5.812 88.540 1426 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.32 % Allowed : 22.97 % Favored : 73.71 % 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: 0.15 (0.24), residues: 1263 helix: 0.78 (0.19), residues: 775 sheet: -1.01 (0.98), residues: 35 loop : -0.90 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B1096 HIS 0.003 0.001 HIS B 574 PHE 0.018 0.001 PHE B 811 TYR 0.017 0.001 TYR B 597 ARG 0.004 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 516) hydrogen bonds : angle 4.39646 ( 1512) covalent geometry : bond 0.00369 (10616) covalent geometry : angle 0.61939 (14405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7083.42 seconds wall clock time: 124 minutes 31.87 seconds (7471.87 seconds total)