Starting phenix.real_space_refine on Wed Feb 4 03:27:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydj_33749/02_2026/7ydj_33749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydj_33749/02_2026/7ydj_33749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ydj_33749/02_2026/7ydj_33749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydj_33749/02_2026/7ydj_33749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ydj_33749/02_2026/7ydj_33749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydj_33749/02_2026/7ydj_33749.map" } resolution = 3.03 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= 0.001 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5589 2.51 5 N 1507 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8751 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1744 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2194 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 5, 'TRANS': 268} Time building chain proxies: 1.65, per 1000 atoms: 0.19 Number of scatterers: 8751 At special positions: 0 Unit cell: (92.4, 119.9, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1595 8.00 N 1507 7.00 C 5589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 612 " - pdb=" SG CYS R 684 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 326.0 milliseconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 38.1% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.840A pdb=" N SER A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 65 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.611A pdb=" N SER A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.586A pdb=" N PHE A 272 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 273 " --> pdb=" O LYS A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 273' Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.838A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.755A pdb=" N TYR A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 364 removed outlier: 4.228A pdb=" N ASN A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 362 " --> pdb=" O GLN A 358 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 4.085A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.677A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.623A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.184A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.914A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 532 through 537 Processing helix chain 'R' and resid 544 through 572 Processing helix chain 'R' and resid 577 through 600 Processing helix chain 'R' and resid 609 through 642 removed outlier: 3.888A pdb=" N ARG R 613 " --> pdb=" O GLY R 609 " (cutoff:3.500A) Processing helix chain 'R' and resid 651 through 674 removed outlier: 3.836A pdb=" N VAL R 662 " --> pdb=" O ILE R 658 " (cutoff:3.500A) Proline residue: R 663 - end of helix removed outlier: 3.515A pdb=" N TYR R 674 " --> pdb=" O SER R 670 " (cutoff:3.500A) Processing helix chain 'R' and resid 675 through 678 removed outlier: 4.009A pdb=" N TYR R 678 " --> pdb=" O SER R 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 675 through 678' Processing helix chain 'R' and resid 688 through 692 removed outlier: 3.514A pdb=" N GLY R 691 " --> pdb=" O PHE R 688 " (cutoff:3.500A) Processing helix chain 'R' and resid 693 through 726 removed outlier: 3.695A pdb=" N LEU R 697 " --> pdb=" O LEU R 693 " (cutoff:3.500A) Proline residue: R 699 - end of helix removed outlier: 3.532A pdb=" N PHE R 702 " --> pdb=" O GLY R 698 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS R 706 " --> pdb=" O PHE R 702 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL R 709 " --> pdb=" O LEU R 705 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL R 712 " --> pdb=" O ALA R 708 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER R 723 " --> pdb=" O THR R 719 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU R 724 " --> pdb=" O GLN R 720 " (cutoff:3.500A) Processing helix chain 'R' and resid 730 through 749 removed outlier: 3.794A pdb=" N THR R 739 " --> pdb=" O ALA R 735 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE R 747 " --> pdb=" O ILE R 743 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU R 748 " --> pdb=" O ALA R 744 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU R 749 " --> pdb=" O GLN R 745 " (cutoff:3.500A) Processing helix chain 'R' and resid 754 through 759 removed outlier: 3.932A pdb=" N ILE R 759 " --> pdb=" O GLY R 756 " (cutoff:3.500A) Processing helix chain 'R' and resid 764 through 776 removed outlier: 3.540A pdb=" N THR R 768 " --> pdb=" O SER R 764 " (cutoff:3.500A) Processing helix chain 'R' and resid 777 through 787 Processing helix chain 'R' and resid 790 through 804 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.261A pdb=" N VAL A 41 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A 243 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 333 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.936A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.027A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.089A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.953A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.996A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.839A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.856A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 7.133A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.296A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.274A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1146 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: 1.04 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2821 1.34 - 1.46: 2189 1.46 - 1.59: 3836 1.59 - 1.71: 0 1.71 - 1.83: 85 Bond restraints: 8931 Sorted by residual: bond pdb=" CB PRO E 224 " pdb=" CG PRO E 224 " ideal model delta sigma weight residual 1.506 1.453 0.053 3.90e-02 6.57e+02 1.88e+00 bond pdb=" SD MET E 218 " pdb=" CE MET E 218 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.49e+00 bond pdb=" CB TRP R 716 " pdb=" CG TRP R 716 " ideal model delta sigma weight residual 1.498 1.461 0.037 3.10e-02 1.04e+03 1.45e+00 bond pdb=" CG LEU R 562 " pdb=" CD2 LEU R 562 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" C ASP A 306 " pdb=" N PRO A 307 " ideal model delta sigma weight residual 1.339 1.375 -0.036 3.40e-02 8.65e+02 1.14e+00 ... (remaining 8926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 11542 1.56 - 3.11: 440 3.11 - 4.67: 71 4.67 - 6.22: 21 6.22 - 7.78: 5 Bond angle restraints: 12079 Sorted by residual: angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 113.39 108.56 4.83 1.47e+00 4.63e-01 1.08e+01 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 108.34 112.57 -4.23 1.31e+00 5.83e-01 1.04e+01 angle pdb=" C LEU B 252 " pdb=" N PHE B 253 " pdb=" CA PHE B 253 " ideal model delta sigma weight residual 122.87 128.07 -5.20 1.61e+00 3.86e-01 1.04e+01 angle pdb=" N SER A 13 " pdb=" CA SER A 13 " pdb=" C SER A 13 " ideal model delta sigma weight residual 108.13 113.63 -5.50 1.72e+00 3.38e-01 1.02e+01 angle pdb=" CA CYS E 147 " pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " ideal model delta sigma weight residual 114.40 121.55 -7.15 2.30e+00 1.89e-01 9.67e+00 ... (remaining 12074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4825 17.53 - 35.06: 398 35.06 - 52.60: 59 52.60 - 70.13: 5 70.13 - 87.66: 3 Dihedral angle restraints: 5290 sinusoidal: 2086 harmonic: 3204 Sorted by residual: dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual -180.00 -154.49 -25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 130.87 -37.87 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CA ALA B 203 " pdb=" C ALA B 203 " pdb=" N CYS B 204 " pdb=" CA CYS B 204 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 692 0.029 - 0.058: 404 0.058 - 0.088: 167 0.088 - 0.117: 84 0.117 - 0.146: 26 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA ASN B 237 " pdb=" N ASN B 237 " pdb=" C ASN B 237 " pdb=" CB ASN B 237 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA ILE A 43 " pdb=" N ILE A 43 " pdb=" C ILE A 43 " pdb=" CB ILE A 43 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA PRO G 49 " pdb=" N PRO G 49 " pdb=" C PRO G 49 " pdb=" CB PRO G 49 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1370 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 680 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO R 681 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO R 681 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 681 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 712 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C VAL R 712 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL R 712 " 0.012 2.00e-02 2.50e+03 pdb=" N THR R 713 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 726 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO R 727 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 727 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 727 " -0.025 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 501 2.73 - 3.27: 8190 3.27 - 3.81: 12943 3.81 - 4.36: 15016 4.36 - 4.90: 26925 Nonbonded interactions: 63575 Sorted by model distance: nonbonded pdb=" OD2 ASP B 298 " pdb=" NZ LYS B 301 " model vdw 2.184 3.120 nonbonded pdb=" N SER R 531 " pdb=" OH TYR R 683 " model vdw 2.262 3.120 nonbonded pdb=" O ASN B 340 " pdb=" NH2 ARG G 62 " model vdw 2.265 3.120 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.270 3.040 nonbonded pdb=" NH2 ARG B 137 " pdb=" O GLU B 172 " model vdw 2.297 3.120 ... (remaining 63570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.100 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.160 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 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 : 0.006 0.053 8933 Z= 0.257 Angle : 0.732 7.780 12083 Z= 0.417 Chirality : 0.047 0.146 1373 Planarity : 0.005 0.053 1519 Dihedral : 12.733 87.660 3216 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.66 (0.25), residues: 1093 helix: 1.01 (0.28), residues: 362 sheet: -0.05 (0.32), residues: 272 loop : -1.89 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 TYR 0.021 0.002 TYR E 178 PHE 0.024 0.003 PHE R 627 TRP 0.016 0.002 TRP B 169 HIS 0.010 0.002 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 8931) covalent geometry : angle 0.73211 (12079) SS BOND : bond 0.01337 ( 2) SS BOND : angle 0.96227 ( 4) hydrogen bonds : bond 0.15104 ( 405) hydrogen bonds : angle 6.05548 ( 1146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.267 Fit side-chains REVERT: A 262 ASP cc_start: 0.6499 (m-30) cc_final: 0.6256 (m-30) REVERT: B 205 ASP cc_start: 0.7186 (t0) cc_final: 0.6881 (t0) REVERT: B 291 ASP cc_start: 0.6365 (m-30) cc_final: 0.5908 (m-30) REVERT: E 211 ASP cc_start: 0.7345 (m-30) cc_final: 0.7143 (m-30) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.1219 time to fit residues: 25.7582 Evaluate side-chains 154 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.0070 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN E 159 ASN G 18 GLN G 24 ASN R 620 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.146767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120744 restraints weight = 12840.597| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.61 r_work: 0.3464 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8933 Z= 0.144 Angle : 0.572 7.383 12083 Z= 0.310 Chirality : 0.043 0.149 1373 Planarity : 0.004 0.050 1519 Dihedral : 4.803 21.009 1202 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.15 % Allowed : 6.27 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.05 (0.26), residues: 1093 helix: 1.89 (0.28), residues: 365 sheet: 0.15 (0.32), residues: 281 loop : -1.85 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 179 TYR 0.015 0.001 TYR B 105 PHE 0.026 0.002 PHE A 273 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8931) covalent geometry : angle 0.57198 (12079) SS BOND : bond 0.01151 ( 2) SS BOND : angle 0.58545 ( 4) hydrogen bonds : bond 0.06209 ( 405) hydrogen bonds : angle 4.50399 ( 1146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.319 Fit side-chains REVERT: A 33 GLU cc_start: 0.7522 (tt0) cc_final: 0.7223 (tt0) REVERT: A 212 PHE cc_start: 0.8069 (p90) cc_final: 0.7654 (p90) REVERT: A 262 ASP cc_start: 0.6916 (m-30) cc_final: 0.6650 (m-30) REVERT: B 61 MET cc_start: 0.8502 (ppp) cc_final: 0.8204 (ppp) REVERT: E 211 ASP cc_start: 0.7418 (m-30) cc_final: 0.7138 (m-30) REVERT: R 721 LYS cc_start: 0.7484 (mmtt) cc_final: 0.7227 (mmmm) outliers start: 11 outliers final: 8 residues processed: 177 average time/residue: 0.1304 time to fit residues: 29.2746 Evaluate side-chains 167 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain R residue 695 SER Chi-restraints excluded: chain R residue 705 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.145238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.119181 restraints weight = 12897.529| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.61 r_work: 0.3444 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8933 Z= 0.165 Angle : 0.576 7.758 12083 Z= 0.310 Chirality : 0.043 0.146 1373 Planarity : 0.004 0.050 1519 Dihedral : 4.724 22.611 1202 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.46 % Allowed : 9.82 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.13 (0.26), residues: 1093 helix: 2.13 (0.28), residues: 365 sheet: 0.26 (0.32), residues: 274 loop : -1.83 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.015 0.002 TYR B 105 PHE 0.019 0.002 PHE A 273 TRP 0.013 0.002 TRP B 82 HIS 0.007 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8931) covalent geometry : angle 0.57591 (12079) SS BOND : bond 0.01124 ( 2) SS BOND : angle 0.48025 ( 4) hydrogen bonds : bond 0.06462 ( 405) hydrogen bonds : angle 4.37774 ( 1146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.327 Fit side-chains REVERT: A 212 PHE cc_start: 0.8122 (p90) cc_final: 0.7690 (p90) REVERT: A 249 ASP cc_start: 0.7398 (t0) cc_final: 0.6994 (t0) REVERT: A 252 ASP cc_start: 0.7406 (t70) cc_final: 0.6787 (m-30) REVERT: A 262 ASP cc_start: 0.6896 (m-30) cc_final: 0.6631 (m-30) REVERT: B 19 ARG cc_start: 0.8157 (ttp-170) cc_final: 0.7744 (ttp-170) REVERT: B 172 GLU cc_start: 0.7315 (tp30) cc_final: 0.7052 (tp30) REVERT: E 207 LEU cc_start: 0.8668 (tt) cc_final: 0.8445 (tp) REVERT: E 208 GLU cc_start: 0.7569 (tp30) cc_final: 0.7353 (tp30) REVERT: E 211 ASP cc_start: 0.7360 (m-30) cc_final: 0.7059 (m-30) outliers start: 14 outliers final: 10 residues processed: 169 average time/residue: 0.1107 time to fit residues: 23.9283 Evaluate side-chains 169 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 695 SER Chi-restraints excluded: chain R residue 705 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 69 optimal weight: 0.0970 chunk 55 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120449 restraints weight = 12951.022| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.62 r_work: 0.3460 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8933 Z= 0.138 Angle : 0.538 7.634 12083 Z= 0.289 Chirality : 0.042 0.142 1373 Planarity : 0.004 0.050 1519 Dihedral : 4.535 20.751 1202 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.46 % Allowed : 11.18 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.26 (0.26), residues: 1093 helix: 2.30 (0.28), residues: 366 sheet: 0.29 (0.32), residues: 272 loop : -1.79 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.010 0.001 TYR R 638 PHE 0.015 0.002 PHE E 200 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8931) covalent geometry : angle 0.53827 (12079) SS BOND : bond 0.01029 ( 2) SS BOND : angle 0.35680 ( 4) hydrogen bonds : bond 0.05747 ( 405) hydrogen bonds : angle 4.23852 ( 1146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.352 Fit side-chains REVERT: A 212 PHE cc_start: 0.8104 (p90) cc_final: 0.7693 (p90) REVERT: A 223 ASP cc_start: 0.7630 (t0) cc_final: 0.7421 (t0) REVERT: A 262 ASP cc_start: 0.6875 (m-30) cc_final: 0.6625 (m-30) REVERT: B 19 ARG cc_start: 0.8139 (ttp-170) cc_final: 0.7723 (ttp-170) REVERT: B 172 GLU cc_start: 0.7357 (tp30) cc_final: 0.7105 (tp30) REVERT: E 211 ASP cc_start: 0.7316 (m-30) cc_final: 0.7039 (m-30) REVERT: R 761 ASP cc_start: 0.6310 (m-30) cc_final: 0.5289 (t0) outliers start: 14 outliers final: 11 residues processed: 167 average time/residue: 0.1271 time to fit residues: 26.9881 Evaluate side-chains 169 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 695 SER Chi-restraints excluded: chain R residue 705 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119051 restraints weight = 12899.788| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.61 r_work: 0.3430 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8933 Z= 0.186 Angle : 0.590 7.703 12083 Z= 0.316 Chirality : 0.044 0.144 1373 Planarity : 0.004 0.049 1519 Dihedral : 4.720 23.369 1202 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.78 % Allowed : 12.02 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.19 (0.26), residues: 1093 helix: 2.21 (0.28), residues: 366 sheet: 0.33 (0.32), residues: 270 loop : -1.84 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.015 0.002 TYR R 638 PHE 0.016 0.002 PHE E 200 TRP 0.019 0.002 TRP B 332 HIS 0.008 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 8931) covalent geometry : angle 0.59004 (12079) SS BOND : bond 0.01210 ( 2) SS BOND : angle 0.58313 ( 4) hydrogen bonds : bond 0.06680 ( 405) hydrogen bonds : angle 4.36927 ( 1146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.8172 (p90) cc_final: 0.7699 (p90) REVERT: A 223 ASP cc_start: 0.7694 (t0) cc_final: 0.7465 (t0) REVERT: A 262 ASP cc_start: 0.6883 (m-30) cc_final: 0.6643 (m-30) REVERT: B 19 ARG cc_start: 0.8143 (ttp-170) cc_final: 0.7736 (ttp-170) REVERT: B 172 GLU cc_start: 0.7465 (tp30) cc_final: 0.7148 (tp30) REVERT: E 164 TRP cc_start: 0.8542 (m100) cc_final: 0.7818 (m100) REVERT: E 211 ASP cc_start: 0.7379 (m-30) cc_final: 0.7085 (m-30) REVERT: R 546 LYS cc_start: 0.7282 (pttt) cc_final: 0.7019 (pttm) outliers start: 17 outliers final: 14 residues processed: 171 average time/residue: 0.1210 time to fit residues: 26.4246 Evaluate side-chains 175 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 695 SER Chi-restraints excluded: chain R residue 705 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.147316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120984 restraints weight = 12923.271| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.66 r_work: 0.3462 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8933 Z= 0.122 Angle : 0.536 8.184 12083 Z= 0.285 Chirality : 0.041 0.140 1373 Planarity : 0.003 0.050 1519 Dihedral : 4.432 19.938 1202 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.57 % Allowed : 13.48 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.39 (0.26), residues: 1093 helix: 2.45 (0.28), residues: 366 sheet: 0.39 (0.32), residues: 271 loop : -1.75 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 643 TYR 0.009 0.001 TYR E 102 PHE 0.015 0.001 PHE E 200 TRP 0.019 0.001 TRP B 332 HIS 0.003 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8931) covalent geometry : angle 0.53651 (12079) SS BOND : bond 0.00998 ( 2) SS BOND : angle 0.40554 ( 4) hydrogen bonds : bond 0.05309 ( 405) hydrogen bonds : angle 4.16907 ( 1146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.241 Fit side-chains REVERT: A 212 PHE cc_start: 0.8109 (p90) cc_final: 0.7694 (p90) REVERT: A 223 ASP cc_start: 0.7654 (t0) cc_final: 0.7412 (t0) REVERT: A 262 ASP cc_start: 0.6847 (m-30) cc_final: 0.6601 (m-30) REVERT: B 19 ARG cc_start: 0.8133 (ttp-170) cc_final: 0.7750 (ttp-170) REVERT: B 332 TRP cc_start: 0.8649 (m-10) cc_final: 0.8332 (m-10) REVERT: E 208 GLU cc_start: 0.7454 (tp30) cc_final: 0.7222 (tp30) REVERT: E 211 ASP cc_start: 0.7251 (m-30) cc_final: 0.6969 (m-30) REVERT: R 687 ASP cc_start: 0.8178 (t0) cc_final: 0.7842 (m-30) outliers start: 15 outliers final: 8 residues processed: 170 average time/residue: 0.1261 time to fit residues: 27.3394 Evaluate side-chains 166 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 133 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119379 restraints weight = 12944.612| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.62 r_work: 0.3445 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8933 Z= 0.168 Angle : 0.578 9.207 12083 Z= 0.307 Chirality : 0.043 0.141 1373 Planarity : 0.004 0.049 1519 Dihedral : 4.570 22.889 1202 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.88 % Allowed : 13.79 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.34 (0.26), residues: 1093 helix: 2.37 (0.28), residues: 367 sheet: 0.39 (0.32), residues: 271 loop : -1.78 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.013 0.002 TYR E 178 PHE 0.030 0.002 PHE A 273 TRP 0.021 0.002 TRP B 332 HIS 0.006 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8931) covalent geometry : angle 0.57806 (12079) SS BOND : bond 0.01185 ( 2) SS BOND : angle 0.53869 ( 4) hydrogen bonds : bond 0.06186 ( 405) hydrogen bonds : angle 4.27420 ( 1146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.7689 (mtm) cc_final: 0.7422 (mtt) REVERT: A 212 PHE cc_start: 0.8156 (p90) cc_final: 0.7690 (p90) REVERT: A 223 ASP cc_start: 0.7682 (t0) cc_final: 0.7413 (t0) REVERT: A 262 ASP cc_start: 0.6851 (m-30) cc_final: 0.6611 (m-30) REVERT: B 19 ARG cc_start: 0.8134 (ttp-170) cc_final: 0.7748 (ttp-170) REVERT: B 332 TRP cc_start: 0.8598 (m-10) cc_final: 0.8355 (m-10) REVERT: E 208 GLU cc_start: 0.7490 (tp30) cc_final: 0.7230 (tp30) REVERT: E 211 ASP cc_start: 0.7357 (m-30) cc_final: 0.7071 (m-30) REVERT: R 687 ASP cc_start: 0.8171 (t0) cc_final: 0.7814 (m-30) outliers start: 18 outliers final: 15 residues processed: 169 average time/residue: 0.1220 time to fit residues: 25.9563 Evaluate side-chains 175 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 678 TYR Chi-restraints excluded: chain R residue 695 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 0.0970 chunk 93 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.148349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122212 restraints weight = 12922.476| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.63 r_work: 0.3481 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8933 Z= 0.115 Angle : 0.536 8.476 12083 Z= 0.282 Chirality : 0.041 0.138 1373 Planarity : 0.003 0.050 1519 Dihedral : 4.319 19.144 1202 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.46 % Allowed : 14.52 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.50 (0.26), residues: 1093 helix: 2.55 (0.28), residues: 367 sheet: 0.39 (0.32), residues: 273 loop : -1.68 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 179 TYR 0.009 0.001 TYR E 102 PHE 0.027 0.001 PHE A 273 TRP 0.021 0.001 TRP B 332 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8931) covalent geometry : angle 0.53609 (12079) SS BOND : bond 0.01029 ( 2) SS BOND : angle 0.36750 ( 4) hydrogen bonds : bond 0.04958 ( 405) hydrogen bonds : angle 4.12417 ( 1146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.7671 (mtm) cc_final: 0.7400 (mtt) REVERT: A 212 PHE cc_start: 0.8107 (p90) cc_final: 0.7693 (p90) REVERT: A 223 ASP cc_start: 0.7641 (t0) cc_final: 0.7371 (t0) REVERT: A 262 ASP cc_start: 0.6827 (m-30) cc_final: 0.6583 (m-30) REVERT: B 19 ARG cc_start: 0.8129 (ttp-170) cc_final: 0.7745 (ttp-170) REVERT: E 25 SER cc_start: 0.8120 (t) cc_final: 0.7804 (p) REVERT: E 98 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7749 (ptt180) REVERT: E 164 TRP cc_start: 0.8608 (m100) cc_final: 0.7878 (m100) REVERT: E 208 GLU cc_start: 0.7474 (tp30) cc_final: 0.7258 (tp30) REVERT: E 211 ASP cc_start: 0.7249 (m-30) cc_final: 0.7019 (m-30) REVERT: R 687 ASP cc_start: 0.8151 (t0) cc_final: 0.7812 (m-30) outliers start: 14 outliers final: 12 residues processed: 173 average time/residue: 0.1280 time to fit residues: 28.2237 Evaluate side-chains 175 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 678 TYR Chi-restraints excluded: chain R residue 695 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.147030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120849 restraints weight = 12939.447| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.63 r_work: 0.3463 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8933 Z= 0.143 Angle : 0.576 8.569 12083 Z= 0.303 Chirality : 0.042 0.143 1373 Planarity : 0.004 0.051 1519 Dihedral : 4.410 21.523 1202 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.57 % Allowed : 14.94 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.47 (0.26), residues: 1093 helix: 2.54 (0.27), residues: 367 sheet: 0.45 (0.32), residues: 268 loop : -1.73 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 179 TYR 0.011 0.001 TYR R 638 PHE 0.025 0.002 PHE A 273 TRP 0.020 0.002 TRP B 332 HIS 0.006 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8931) covalent geometry : angle 0.57605 (12079) SS BOND : bond 0.01105 ( 2) SS BOND : angle 0.47551 ( 4) hydrogen bonds : bond 0.05570 ( 405) hydrogen bonds : angle 4.25052 ( 1146) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.343 Fit side-chains REVERT: A 25 MET cc_start: 0.7695 (mtm) cc_final: 0.7429 (mtt) REVERT: A 212 PHE cc_start: 0.8135 (p90) cc_final: 0.7677 (p90) REVERT: A 223 ASP cc_start: 0.7652 (t0) cc_final: 0.7432 (t0) REVERT: A 262 ASP cc_start: 0.6831 (m-30) cc_final: 0.6589 (m-30) REVERT: B 19 ARG cc_start: 0.8138 (ttp-170) cc_final: 0.7759 (ttp-170) REVERT: B 332 TRP cc_start: 0.8529 (m-10) cc_final: 0.8145 (m-10) REVERT: E 98 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7723 (ptt180) REVERT: E 211 ASP cc_start: 0.7271 (m-30) cc_final: 0.6958 (m-30) outliers start: 15 outliers final: 11 residues processed: 168 average time/residue: 0.1393 time to fit residues: 29.7076 Evaluate side-chains 173 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 695 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 0.0070 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.145673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119581 restraints weight = 12911.161| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.63 r_work: 0.3446 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8933 Z= 0.166 Angle : 0.614 10.029 12083 Z= 0.321 Chirality : 0.043 0.143 1373 Planarity : 0.004 0.050 1519 Dihedral : 4.522 22.199 1202 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.36 % Allowed : 15.26 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.41 (0.26), residues: 1093 helix: 2.46 (0.28), residues: 367 sheet: 0.35 (0.31), residues: 278 loop : -1.74 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 148 TYR 0.012 0.002 TYR R 638 PHE 0.031 0.002 PHE E 227 TRP 0.012 0.002 TRP A 234 HIS 0.006 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8931) covalent geometry : angle 0.61352 (12079) SS BOND : bond 0.01412 ( 2) SS BOND : angle 0.81977 ( 4) hydrogen bonds : bond 0.06069 ( 405) hydrogen bonds : angle 4.32652 ( 1146) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.7708 (mtm) cc_final: 0.7442 (mtt) REVERT: A 212 PHE cc_start: 0.8170 (p90) cc_final: 0.7717 (p90) REVERT: A 223 ASP cc_start: 0.7689 (t0) cc_final: 0.7447 (t0) REVERT: A 262 ASP cc_start: 0.6833 (m-30) cc_final: 0.6597 (m-30) REVERT: B 19 ARG cc_start: 0.8087 (ttp-170) cc_final: 0.7707 (ttp-170) REVERT: E 25 SER cc_start: 0.8150 (t) cc_final: 0.7815 (p) REVERT: E 211 ASP cc_start: 0.7242 (m-30) cc_final: 0.6914 (m-30) REVERT: R 687 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7952 (m-30) outliers start: 13 outliers final: 11 residues processed: 172 average time/residue: 0.1417 time to fit residues: 30.7347 Evaluate side-chains 177 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 687 ASP Chi-restraints excluded: chain R residue 695 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 0.0050 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.147189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120994 restraints weight = 12809.268| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.61 r_work: 0.3464 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8933 Z= 0.136 Angle : 0.589 12.379 12083 Z= 0.306 Chirality : 0.042 0.139 1373 Planarity : 0.004 0.051 1519 Dihedral : 4.392 21.044 1202 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.36 % Allowed : 15.88 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.49 (0.26), residues: 1093 helix: 2.55 (0.28), residues: 367 sheet: 0.45 (0.32), residues: 272 loop : -1.74 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 148 TYR 0.010 0.001 TYR E 50 PHE 0.029 0.002 PHE E 227 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8931) covalent geometry : angle 0.58857 (12079) SS BOND : bond 0.01193 ( 2) SS BOND : angle 0.78908 ( 4) hydrogen bonds : bond 0.05400 ( 405) hydrogen bonds : angle 4.22713 ( 1146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2070.40 seconds wall clock time: 36 minutes 9.77 seconds (2169.77 seconds total)