Starting phenix.real_space_refine on Thu Jul 2 22:22:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dd7_27335/07_2026/8dd7_27335.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dd7_27335/07_2026/8dd7_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dd7_27335/07_2026/8dd7_27335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dd7_27335/07_2026/8dd7_27335.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dd7_27335/07_2026/8dd7_27335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dd7_27335/07_2026/8dd7_27335.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dd7_27335/07_2026/8dd7_27335.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dd7_27335/07_2026/8dd7_27335.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 2.33, per 1000 atoms: 0.22 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: 1.02 Conformation dependent library (CDL) restraints added in 397.6 milliseconds 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: 0.42 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: 1.51 Time building geometry restraints manager: 1.34 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: 5383 17.85 - 35.70: 702 35.70 - 53.55: 195 53.55 - 71.40: 37 71.40 - 89.25: 15 Dihedral angle restraints: 6332 sinusoidal: 2605 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 6329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1371 0.068 - 0.136: 202 0.136 - 0.204: 29 0.204 - 0.273: 2 0.273 - 0.341: 1 Chirality restraints: 1605 Sorted by residual: chirality pdb=" CA MET B1038 " pdb=" N MET B1038 " pdb=" C MET B1038 " pdb=" CB MET B1038 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB THR B 626 " pdb=" CA THR B 626 " pdb=" OG1 THR B 626 " pdb=" CG2 THR B 626 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE B 642 " pdb=" CA ILE B 642 " pdb=" CG1 ILE B 642 " pdb=" CG2 ILE B 642 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1602 not shown) Planarity restraints: 1827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1216 " -0.864 9.50e-02 1.11e+02 3.87e-01 9.11e+01 pdb=" NE ARG B1216 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG B1216 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B1216 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B1216 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1210 " 0.031 2.00e-02 2.50e+03 1.90e-02 9.00e+00 pdb=" CG TRP B1210 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B1210 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B1210 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1210 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B1210 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B1210 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1210 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1210 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B1210 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 850 " 0.018 2.00e-02 2.50e+03 1.80e-02 8.12e+00 pdb=" CG TRP B 850 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 850 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 850 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 850 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 850 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 850 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 850 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 850 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 850 " 0.002 2.00e-02 2.50e+03 ... (remaining 1824 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2731 2.80 - 3.32: 10040 3.32 - 3.85: 17587 3.85 - 4.37: 20295 4.37 - 4.90: 33540 Nonbonded interactions: 84193 Sorted by model distance: nonbonded pdb=" OG1 THR B 577 " pdb=" OD1 ASP B 579 " model vdw 2.272 3.040 nonbonded pdb=" O LEU B 209 " pdb=" OG1 THR B 213 " model vdw 2.275 3.040 nonbonded pdb=" O SER B 777 " pdb=" OG1 THR B 781 " model vdw 2.283 3.040 nonbonded pdb=" ND2 ASN B 701 " pdb=" OE1 GLN B 718 " model vdw 2.296 3.120 nonbonded pdb=" O SER B1130 " pdb=" OG SER B1130 " model vdw 2.296 3.040 ... (remaining 84188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.000 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 17.519 89.249 3916 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.22 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG A 294 TYR 0.020 0.001 TYR B1095 PHE 0.034 0.002 PHE B 811 TRP 0.050 0.002 TRP B1210 HIS 0.006 0.001 HIS B1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.26 (10616) covalent geometry : angle 0.94380 / 0.51 (14405) hydrogen bonds : bond 0.22333 / 14.96 ( 516) hydrogen bonds : angle 7.75510 / 5.61 ( 1512) *********************** 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 : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8624 (tp) cc_final: 0.8383 (tp) REVERT: A 270 LEU cc_start: 0.8667 (tt) cc_final: 0.8181 (mp) REVERT: B 179 MET cc_start: 0.4315 (ptt) cc_final: 0.4045 (ptt) REVERT: B 185 MET cc_start: 0.6852 (mmm) cc_final: 0.6338 (mmm) REVERT: B 211 LEU cc_start: 0.8697 (tp) cc_final: 0.8384 (mt) REVERT: B 789 MET cc_start: 0.5516 (mmt) cc_final: 0.4917 (mmm) REVERT: B 813 MET cc_start: 0.6151 (tmm) cc_final: 0.5623 (tmm) REVERT: B 814 MET cc_start: 0.7873 (mmt) cc_final: 0.7356 (mmp) REVERT: B 1075 HIS cc_start: 0.8218 (p90) cc_final: 0.7939 (p-80) outliers start: 5 outliers final: 0 residues processed: 112 average time/residue: 0.0927 time to fit residues: 15.0017 Evaluate side-chains 90 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS ** 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 = 0.4095 r_free = 0.4095 target = 0.122243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.086995 restraints weight = 25413.226| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 4.07 r_work: 0.3175 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10616 Z= 0.194 Angle : 0.675 8.006 14405 Z= 0.343 Chirality : 0.043 0.166 1605 Planarity : 0.005 0.049 1827 Dihedral : 5.928 77.735 1383 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.58 % Allowed : 21.57 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1263 helix: -0.24 (0.18), residues: 770 sheet: -0.38 (1.10), residues: 35 loop : -1.41 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 278 TYR 0.019 0.002 TYR B1043 PHE 0.030 0.002 PHE B 811 TRP 0.022 0.002 TRP B1210 HIS 0.005 0.001 HIS B1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (10616) covalent geometry : angle 0.67544 / 0.34 (14405) hydrogen bonds : bond 0.04730 / 3.05 ( 516) hydrogen bonds : angle 5.05742 / 3.64 ( 1512) *********************** 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 129 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8638 (tpp-160) REVERT: A 90 TYR cc_start: 0.8852 (t80) cc_final: 0.8646 (t80) REVERT: B 179 MET cc_start: 0.4677 (ptt) cc_final: 0.4436 (ptt) REVERT: B 814 MET cc_start: 0.8005 (mmt) cc_final: 0.7697 (mmp) REVERT: B 1038 MET cc_start: 0.5679 (ttm) cc_final: 0.5001 (tpt) outliers start: 41 outliers final: 18 residues processed: 123 average time/residue: 0.0905 time to fit residues: 16.1780 Evaluate side-chains 96 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 139 THR 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 376 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 779 HIS 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 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 101 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1012 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.124039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.088618 restraints weight = 25374.866| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.75 r_work: 0.3204 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2004 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= 0.140 Angle : 0.600 7.905 14405 Z= 0.306 Chirality : 0.041 0.202 1605 Planarity : 0.004 0.062 1827 Dihedral : 5.716 80.192 1383 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.23 % Allowed : 22.79 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.24), residues: 1263 helix: 0.29 (0.18), residues: 775 sheet: -0.56 (1.07), residues: 35 loop : -1.26 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1091 TYR 0.016 0.001 TYR B1095 PHE 0.032 0.001 PHE B 811 TRP 0.018 0.002 TRP B1210 HIS 0.006 0.001 HIS B1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10616) covalent geometry : angle 0.60033 / 0.31 (14405) hydrogen bonds : bond 0.04024 / 2.59 ( 516) hydrogen bonds : angle 4.72899 / 3.39 ( 1512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.420 Fit side-chains REVERT: A 58 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8620 (tpp-160) REVERT: A 90 TYR cc_start: 0.8922 (t80) cc_final: 0.8692 (t80) REVERT: B 179 MET cc_start: 0.4715 (ptt) cc_final: 0.4503 (ptt) REVERT: B 191 MET cc_start: 0.7222 (ttp) cc_final: 0.6953 (ttp) REVERT: B 724 MET cc_start: 0.7571 (tpp) cc_final: 0.7160 (tpp) REVERT: B 734 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6816 (mm) REVERT: B 814 MET cc_start: 0.8116 (mmt) cc_final: 0.7747 (mmp) REVERT: B 850 TRP cc_start: 0.5779 (p90) cc_final: 0.5369 (m-90) REVERT: B 1102 TYR cc_start: 0.4762 (OUTLIER) cc_final: 0.4250 (p90) outliers start: 37 outliers final: 19 residues processed: 115 average time/residue: 0.0968 time to fit residues: 16.4255 Evaluate side-chains 98 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 727 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 115 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 100 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 720 GLN ** 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 = 0.4065 r_free = 0.4065 target = 0.119760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.083209 restraints weight = 25391.699| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.11 r_work: 0.3171 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- 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 = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10616 Z= 0.171 Angle : 0.615 8.253 14405 Z= 0.310 Chirality : 0.042 0.251 1605 Planarity : 0.004 0.057 1827 Dihedral : 5.691 85.737 1383 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.97 % Allowed : 23.93 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.25), residues: 1263 helix: 0.53 (0.19), residues: 763 sheet: -0.79 (1.03), residues: 35 loop : -1.19 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.019 0.002 TYR B 597 PHE 0.034 0.002 PHE B 811 TRP 0.014 0.002 TRP B1210 HIS 0.004 0.001 HIS B1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (10616) covalent geometry : angle 0.61478 / 0.31 (14405) hydrogen bonds : bond 0.03853 / 2.51 ( 516) hydrogen bonds : angle 4.62620 / 3.29 ( 1512) *********************** 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 110 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.438 Fit side-chains REVERT: A 58 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8555 (tpp-160) REVERT: B 714 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7759 (mp) REVERT: B 734 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6838 (mm) REVERT: B 814 MET cc_start: 0.8083 (mmt) cc_final: 0.7771 (mmp) REVERT: B 850 TRP cc_start: 0.5835 (p90) cc_final: 0.5432 (m-90) REVERT: B 1102 TYR cc_start: 0.4823 (OUTLIER) cc_final: 0.4257 (p90) outliers start: 34 outliers final: 21 residues processed: 109 average time/residue: 0.1065 time to fit residues: 16.9163 Evaluate side-chains 96 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 338 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 26 VAL 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 1073 LEU Chi-restraints excluded: chain B residue 1102 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 241 GLN B 782 GLN ** 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 = 0.3996 r_free = 0.3996 target = 0.116245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076985 restraints weight = 25477.769| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.87 r_work: 0.3077 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 10616 Z= 0.309 Angle : 0.731 9.483 14405 Z= 0.366 Chirality : 0.047 0.340 1605 Planarity : 0.005 0.054 1827 Dihedral : 5.763 62.212 1383 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.98 % Allowed : 22.62 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.24), residues: 1263 helix: 0.19 (0.18), residues: 773 sheet: -1.25 (0.98), residues: 35 loop : -1.28 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 271 TYR 0.030 0.002 TYR B 597 PHE 0.029 0.002 PHE B 811 TRP 0.013 0.002 TRP A 342 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.31 (10616) covalent geometry : angle 0.73100 / 0.37 (14405) hydrogen bonds : bond 0.04529 / 3.00 ( 516) hydrogen bonds : angle 4.90831 / 3.46 ( 1512) *********************** 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 133 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 76 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8557 (tpp-160) REVERT: A 357 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7954 (mp10) REVERT: B 734 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7030 (mm) REVERT: B 850 TRP cc_start: 0.5965 (p90) cc_final: 0.5241 (m-90) REVERT: B 1102 TYR cc_start: 0.5022 (OUTLIER) cc_final: 0.4391 (p90) outliers start: 57 outliers final: 29 residues processed: 127 average time/residue: 0.1033 time to fit residues: 19.1704 Evaluate side-chains 104 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 291 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1039 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 75 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 107 optimal weight: 10.0000 chunk 108 optimal weight: 0.0170 chunk 11 optimal weight: 0.0000 overall best weight: 0.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 ASN B 718 GLN ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.119830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.084655 restraints weight = 25137.043| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 4.11 r_work: 0.3133 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10616 Z= 0.127 Angle : 0.618 16.500 14405 Z= 0.305 Chirality : 0.042 0.271 1605 Planarity : 0.004 0.062 1827 Dihedral : 5.587 69.413 1383 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.41 % Allowed : 24.10 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.24), residues: 1263 helix: 0.53 (0.19), residues: 775 sheet: -1.14 (0.99), residues: 35 loop : -1.12 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 56 TYR 0.017 0.001 TYR B1095 PHE 0.036 0.001 PHE B 811 TRP 0.019 0.001 TRP B1096 HIS 0.004 0.001 HIS B 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (10616) covalent geometry : angle 0.61785 / 0.30 (14405) hydrogen bonds : bond 0.03728 / 2.43 ( 516) hydrogen bonds : angle 4.60180 / 3.27 ( 1512) *********************** 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 118 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8587 (tpp-160) REVERT: A 357 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: B 734 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.7028 (mm) REVERT: B 789 MET cc_start: 0.6562 (mmt) cc_final: 0.5915 (mmm) REVERT: B 813 MET cc_start: 0.6907 (tpp) cc_final: 0.6365 (ttt) REVERT: B 850 TRP cc_start: 0.5923 (p90) cc_final: 0.5249 (m-90) REVERT: B 1102 TYR cc_start: 0.4994 (OUTLIER) cc_final: 0.4377 (p90) outliers start: 39 outliers final: 28 residues processed: 113 average time/residue: 0.1031 time to fit residues: 16.6892 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 : 0.415 ------------------------------------------------------------------------------- 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 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 218 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 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.0370 chunk 33 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 GLN ** 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 = 0.4045 r_free = 0.4045 target = 0.119410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.082831 restraints weight = 25015.759| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.19 r_work: 0.3146 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10616 Z= 0.119 Angle : 0.606 12.900 14405 Z= 0.300 Chirality : 0.041 0.237 1605 Planarity : 0.004 0.061 1827 Dihedral : 5.418 70.125 1383 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.32 % Allowed : 24.28 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1263 helix: 0.68 (0.19), residues: 775 sheet: -1.07 (0.99), residues: 35 loop : -1.02 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 12 TYR 0.018 0.001 TYR B1095 PHE 0.034 0.001 PHE B 811 TRP 0.044 0.002 TRP B1096 HIS 0.003 0.000 HIS B 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10616) covalent geometry : angle 0.60620 / 0.30 (14405) hydrogen bonds : bond 0.03563 / 2.32 ( 516) hydrogen bonds : angle 4.52724 / 3.21 ( 1512) *********************** 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 116 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8561 (tpp-160) REVERT: A 357 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8031 (mp10) REVERT: B 80 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8631 (pt0) REVERT: B 730 LEU cc_start: 0.7977 (tp) cc_final: 0.7751 (tp) REVERT: B 734 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6878 (mm) REVERT: B 789 MET cc_start: 0.6455 (mmt) cc_final: 0.6007 (mmm) REVERT: B 813 MET cc_start: 0.6803 (tpp) cc_final: 0.6375 (ttt) REVERT: B 850 TRP cc_start: 0.5897 (p90) cc_final: 0.5173 (m-90) REVERT: B 1102 TYR cc_start: 0.5103 (OUTLIER) cc_final: 0.4502 (p90) outliers start: 38 outliers final: 25 residues processed: 112 average time/residue: 0.0888 time to fit residues: 14.8715 Evaluate side-chains 104 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 706 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 GLN ** 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 = 0.4041 r_free = 0.4041 target = 0.119187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.083515 restraints weight = 25035.814| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.22 r_work: 0.3134 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3320 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= 0.131 Angle : 0.609 11.786 14405 Z= 0.301 Chirality : 0.041 0.271 1605 Planarity : 0.004 0.058 1827 Dihedral : 5.268 68.061 1383 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.06 % Allowed : 24.54 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1263 helix: 0.72 (0.19), residues: 771 sheet: -1.06 (0.98), residues: 35 loop : -1.02 (0.32), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 56 TYR 0.015 0.001 TYR B1095 PHE 0.030 0.001 PHE B 811 TRP 0.031 0.001 TRP B1096 HIS 0.003 0.001 HIS B 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10616) covalent geometry : angle 0.60900 / 0.30 (14405) hydrogen bonds : bond 0.03554 / 2.32 ( 516) hydrogen bonds : angle 4.50691 / 3.20 ( 1512) *********************** 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 111 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8596 (tpp-160) REVERT: A 357 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8033 (mp10) REVERT: B 80 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8652 (pt0) REVERT: B 182 MET cc_start: 0.6551 (tpt) cc_final: 0.6320 (pmm) REVERT: B 730 LEU cc_start: 0.8019 (tp) cc_final: 0.7809 (tp) REVERT: B 789 MET cc_start: 0.6506 (mmt) cc_final: 0.6026 (mmm) REVERT: B 813 MET cc_start: 0.6866 (tpp) cc_final: 0.6390 (ttt) REVERT: B 850 TRP cc_start: 0.5987 (p90) cc_final: 0.5222 (m-90) REVERT: B 1038 MET cc_start: 0.5531 (tpt) cc_final: 0.5141 (tpt) REVERT: B 1043 TYR cc_start: 0.8762 (t80) cc_final: 0.8542 (t80) REVERT: B 1102 TYR cc_start: 0.5001 (OUTLIER) cc_final: 0.4399 (p90) outliers start: 35 outliers final: 24 residues processed: 107 average time/residue: 0.1131 time to fit residues: 17.1971 Evaluate side-chains 101 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 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 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 168 LEU 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 788 VAL 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 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 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 87 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 0.2980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** 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 = 0.4045 r_free = 0.4045 target = 0.119443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.085935 restraints weight = 25184.891| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.80 r_work: 0.3113 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10616 Z= 0.126 Angle : 0.609 11.462 14405 Z= 0.298 Chirality : 0.041 0.255 1605 Planarity : 0.004 0.056 1827 Dihedral : 5.174 67.386 1383 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.14 % Allowed : 24.37 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.25), residues: 1263 helix: 0.77 (0.19), residues: 770 sheet: -0.92 (0.98), residues: 35 loop : -0.97 (0.32), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 736 TYR 0.015 0.001 TYR B1095 PHE 0.028 0.001 PHE B 811 TRP 0.029 0.001 TRP B1096 HIS 0.007 0.001 HIS B 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (10616) covalent geometry : angle 0.60916 / 0.30 (14405) hydrogen bonds : bond 0.03484 / 2.28 ( 516) hydrogen bonds : angle 4.45764 / 3.16 ( 1512) *********************** 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 115 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8638 (tpp-160) REVERT: A 357 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: B 80 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8702 (pt0) REVERT: B 182 MET cc_start: 0.6821 (tpt) cc_final: 0.6594 (pmm) REVERT: B 789 MET cc_start: 0.6606 (mmt) cc_final: 0.6254 (mmm) REVERT: B 792 TYR cc_start: 0.7291 (m-80) cc_final: 0.7025 (m-80) REVERT: B 795 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8700 (mp) REVERT: B 813 MET cc_start: 0.6891 (tpp) cc_final: 0.6328 (ttt) REVERT: B 850 TRP cc_start: 0.5975 (p90) cc_final: 0.5175 (m-90) REVERT: B 1102 TYR cc_start: 0.4848 (OUTLIER) cc_final: 0.4263 (p90) outliers start: 36 outliers final: 28 residues processed: 110 average time/residue: 0.1036 time to fit residues: 16.4524 Evaluate side-chains 108 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 315 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 643 ASP 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 788 VAL Chi-restraints excluded: chain B residue 795 LEU 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 1074 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 62 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.0060 chunk 21 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 ASN B 718 GLN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.119780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.081252 restraints weight = 24958.703| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.89 r_work: 0.3167 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10616 Z= 0.122 Angle : 0.612 11.461 14405 Z= 0.300 Chirality : 0.042 0.250 1605 Planarity : 0.004 0.056 1827 Dihedral : 5.110 67.146 1383 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.53 % Allowed : 24.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1263 helix: 0.78 (0.19), residues: 778 sheet: -0.95 (0.97), residues: 35 loop : -0.97 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 56 TYR 0.013 0.001 TYR B1095 PHE 0.025 0.001 PHE B 811 TRP 0.029 0.001 TRP B1096 HIS 0.006 0.001 HIS B 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10616) covalent geometry : angle 0.61227 / 0.30 (14405) hydrogen bonds : bond 0.03445 / 2.24 ( 516) hydrogen bonds : angle 4.44224 / 3.15 ( 1512) ********************** 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 107 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8545 (tpp-160) REVERT: A 357 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: B 182 MET cc_start: 0.6937 (tpt) cc_final: 0.6664 (pmm) REVERT: B 789 MET cc_start: 0.6609 (mmt) cc_final: 0.6083 (mmm) REVERT: B 813 MET cc_start: 0.6834 (tpp) cc_final: 0.6223 (ttt) REVERT: B 850 TRP cc_start: 0.5948 (p90) cc_final: 0.5081 (m-90) REVERT: B 1096 TRP cc_start: 0.5764 (m100) cc_final: 0.5559 (m100) REVERT: B 1102 TYR cc_start: 0.4820 (OUTLIER) cc_final: 0.4231 (p90) outliers start: 29 outliers final: 24 residues processed: 101 average time/residue: 0.0980 time to fit residues: 14.5656 Evaluate side-chains 103 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 156 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 285 HIS 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 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 643 ASP 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 1023 LEU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1074 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 121 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.118771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082446 restraints weight = 25232.427| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.46 r_work: 0.3118 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10616 Z= 0.156 Angle : 0.636 11.382 14405 Z= 0.313 Chirality : 0.042 0.290 1605 Planarity : 0.004 0.054 1827 Dihedral : 5.080 64.391 1383 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.45 % Allowed : 25.33 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1263 helix: 0.69 (0.19), residues: 783 sheet: -0.91 (0.98), residues: 35 loop : -0.94 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 194 TYR 0.015 0.001 TYR B 597 PHE 0.036 0.001 PHE B 811 TRP 0.026 0.001 TRP B1096 HIS 0.024 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (10616) covalent geometry : angle 0.63649 / 0.31 (14405) hydrogen bonds : bond 0.03608 / 2.37 ( 516) hydrogen bonds : angle 4.48728 / 3.19 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2684.04 seconds wall clock time: 46 minutes 51.93 seconds (2811.93 seconds total)