Starting phenix.real_space_refine on Fri Aug 22 21:41:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydm_33753/08_2025/7ydm_33753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydm_33753/08_2025/7ydm_33753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ydm_33753/08_2025/7ydm_33753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydm_33753/08_2025/7ydm_33753.map" model { file = "/net/cci-nas-00/data/ceres_data/7ydm_33753/08_2025/7ydm_33753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydm_33753/08_2025/7ydm_33753.cif" } resolution = 2.89 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= 0.022 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 55 5.16 5 C 5170 2.51 5 N 1410 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8131 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1928 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 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: "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: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} 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: 0.20 Number of scatterers: 8131 At special positions: 0 Unit cell: (79.2, 104.5, 136.4, 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 55 16.00 O 1496 8.00 N 1410 7.00 C 5170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 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: 0.44 Conformation dependent library (CDL) restraints added in 312.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 39.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.637A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.525A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.530A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.601A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.615A pdb=" N ASP A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.575A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.731A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.847A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 22 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.628A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.699A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'R' and resid 532 through 537 removed outlier: 3.708A pdb=" N LEU R 536 " --> pdb=" O PHE R 533 " (cutoff:3.500A) Processing helix chain 'R' and resid 544 through 572 removed outlier: 3.657A pdb=" N THR R 548 " --> pdb=" O ASP R 544 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU R 549 " --> pdb=" O TRP R 545 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE R 550 " --> pdb=" O LYS R 546 " (cutoff:3.500A) Processing helix chain 'R' and resid 577 through 601 removed outlier: 3.530A pdb=" N ILE R 601 " --> pdb=" O PHE R 597 " (cutoff:3.500A) Processing helix chain 'R' and resid 609 through 642 removed outlier: 3.546A pdb=" N ARG R 613 " --> pdb=" O GLY R 609 " (cutoff:3.500A) Processing helix chain 'R' and resid 651 through 674 removed outlier: 3.576A pdb=" N TYR R 660 " --> pdb=" O CYS R 656 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL R 662 " --> pdb=" O ILE R 658 " (cutoff:3.500A) Proline residue: R 663 - end of helix Processing helix chain 'R' and resid 688 through 692 Processing helix chain 'R' and resid 693 through 720 Proline residue: R 699 - end of helix removed outlier: 3.530A pdb=" N PHE R 702 " --> pdb=" O GLY R 698 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE R 703 " --> pdb=" O PRO R 699 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL R 709 " --> pdb=" O LEU R 705 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL R 712 " --> pdb=" O ALA R 708 " (cutoff:3.500A) Processing helix chain 'R' and resid 721 through 726 Processing helix chain 'R' and resid 733 through 747 removed outlier: 4.032A pdb=" N ALA R 737 " --> pdb=" O LYS R 733 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU R 738 " --> pdb=" O LYS R 734 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR R 739 " --> pdb=" O ALA R 735 " (cutoff:3.500A) Processing helix chain 'R' and resid 751 through 759 removed outlier: 4.017A pdb=" N PHE R 755 " --> pdb=" O THR R 752 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE R 758 " --> pdb=" O PHE R 755 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE R 759 " --> pdb=" O GLY R 756 " (cutoff:3.500A) Processing helix chain 'R' and resid 765 through 776 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 207 through 214 removed outlier: 6.424A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.866A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.019A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.074A 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: 6.801A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.017A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.022A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.230A 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: 6.989A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.549A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.049A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG N 38 " --> pdb=" O GLU N 46 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1038 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: 1.19 Time building geometry restraints manager: 0.58 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: 2541 1.34 - 1.45: 1217 1.45 - 1.57: 4464 1.57 - 1.69: 0 1.69 - 1.81: 73 Bond restraints: 8295 Sorted by residual: bond pdb=" CA ASP R 541 " pdb=" CB ASP R 541 " ideal model delta sigma weight residual 1.527 1.549 -0.022 1.61e-02 3.86e+03 1.81e+00 bond pdb=" C ILE B 93 " pdb=" N PRO B 94 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.23e-02 6.61e+03 1.74e+00 bond pdb=" CG LEU A 46 " pdb=" CD1 LEU A 46 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" CB GLN A 385 " pdb=" CG GLN A 385 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" C GLN A 31 " pdb=" O GLN A 31 " ideal model delta sigma weight residual 1.236 1.249 -0.013 1.15e-02 7.56e+03 1.27e+00 ... (remaining 8290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 10896 1.81 - 3.62: 284 3.62 - 5.42: 40 5.42 - 7.23: 6 7.23 - 9.04: 2 Bond angle restraints: 11228 Sorted by residual: angle pdb=" N CYS R 751 " pdb=" CA CYS R 751 " pdb=" C CYS R 751 " ideal model delta sigma weight residual 114.62 109.86 4.76 1.14e+00 7.69e-01 1.74e+01 angle pdb=" N ARG A 389 " pdb=" CA ARG A 389 " pdb=" C ARG A 389 " ideal model delta sigma weight residual 114.04 109.28 4.76 1.24e+00 6.50e-01 1.47e+01 angle pdb=" N GLY R 600 " pdb=" CA GLY R 600 " pdb=" C GLY R 600 " ideal model delta sigma weight residual 113.18 121.60 -8.42 2.37e+00 1.78e-01 1.26e+01 angle pdb=" C VAL R 641 " pdb=" N VAL R 642 " pdb=" CA VAL R 642 " ideal model delta sigma weight residual 122.97 119.76 3.21 9.80e-01 1.04e+00 1.07e+01 angle pdb=" C VAL N 48 " pdb=" N SER N 49 " pdb=" CA SER N 49 " ideal model delta sigma weight residual 121.75 116.18 5.57 1.73e+00 3.34e-01 1.04e+01 ... (remaining 11223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 4459 16.71 - 33.43: 375 33.43 - 50.14: 65 50.14 - 66.85: 16 66.85 - 83.56: 8 Dihedral angle restraints: 4923 sinusoidal: 1940 harmonic: 2983 Sorted by residual: 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 180.00 147.18 32.82 0 5.00e+00 4.00e-02 4.31e+01 dihedral pdb=" CA LEU R 705 " pdb=" C LEU R 705 " pdb=" N CYS R 706 " pdb=" CA CYS R 706 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CB CYS R 612 " pdb=" SG CYS R 612 " pdb=" SG CYS R 684 " pdb=" CB CYS R 684 " ideal model delta sinusoidal sigma weight residual -86.00 -130.61 44.61 1 1.00e+01 1.00e-02 2.77e+01 ... (remaining 4920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 848 0.045 - 0.089: 324 0.089 - 0.134: 86 0.134 - 0.178: 9 0.178 - 0.223: 2 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA ASP R 541 " pdb=" N ASP R 541 " pdb=" C ASP R 541 " pdb=" CB ASP R 541 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE R 759 " pdb=" CA ILE R 759 " pdb=" CG1 ILE R 759 " pdb=" CG2 ILE R 759 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 1266 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 726 " 0.083 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO R 727 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO R 727 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO R 727 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 680 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO R 681 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 681 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 681 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO G 53 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.034 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 111 2.67 - 3.23: 7169 3.23 - 3.79: 11172 3.79 - 4.34: 14860 4.34 - 4.90: 25710 Nonbonded interactions: 59022 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.115 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.188 3.040 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR R 674 " pdb=" NZ LYS R 676 " model vdw 2.290 3.120 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.298 3.040 ... (remaining 59017 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.000 Find NCS groups from input model: 0.030 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:8.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.007 0.048 8296 Z= 0.287 Angle : 0.725 9.039 11230 Z= 0.426 Chirality : 0.049 0.223 1269 Planarity : 0.006 0.124 1424 Dihedral : 13.257 83.565 2996 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -0.11 (0.26), residues: 1019 helix: 0.98 (0.27), residues: 366 sheet: 0.77 (0.34), residues: 238 loop : -1.58 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 336 TYR 0.013 0.002 TYR N 95 PHE 0.025 0.003 PHE N 108 TRP 0.022 0.002 TRP A 234 HIS 0.014 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00680 ( 8295) covalent geometry : angle 0.72461 (11228) SS BOND : bond 0.00112 ( 1) SS BOND : angle 1.05804 ( 2) hydrogen bonds : bond 0.15789 ( 371) hydrogen bonds : angle 5.79118 ( 1038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.211 Fit side-chains REVERT: A 221 MET cc_start: 0.8534 (ttm) cc_final: 0.8169 (ttp) REVERT: A 251 SER cc_start: 0.8728 (p) cc_final: 0.8329 (t) REVERT: A 309 GLU cc_start: 0.7299 (pm20) cc_final: 0.7027 (pm20) REVERT: A 390 GLU cc_start: 0.7313 (tp30) cc_final: 0.7060 (tp30) REVERT: B 189 SER cc_start: 0.7771 (m) cc_final: 0.7529 (m) REVERT: B 262 MET cc_start: 0.6975 (tpp) cc_final: 0.6444 (tpp) REVERT: B 281 SER cc_start: 0.8507 (p) cc_final: 0.8267 (p) REVERT: G 21 MET cc_start: 0.7616 (tpp) cc_final: 0.7241 (tpp) REVERT: R 733 LYS cc_start: 0.8240 (mmpt) cc_final: 0.8017 (mmpt) REVERT: R 775 ASN cc_start: 0.8445 (m-40) cc_final: 0.8046 (m-40) outliers start: 0 outliers final: 1 residues processed: 179 average time/residue: 0.5326 time to fit residues: 100.4314 Evaluate side-chains 160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 759 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 292 ASN A 385 GLN B 75 GLN B 155 ASN B 268 ASN R 745 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102078 restraints weight = 11649.717| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.14 r_work: 0.3191 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8296 Z= 0.171 Angle : 0.579 7.711 11230 Z= 0.322 Chirality : 0.044 0.184 1269 Planarity : 0.005 0.073 1424 Dihedral : 4.733 29.987 1125 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.04 % Allowed : 8.28 % Favored : 89.68 % 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 aren not related in a simple way. whole: 0.33 (0.27), residues: 1019 helix: 1.60 (0.28), residues: 369 sheet: 0.85 (0.33), residues: 246 loop : -1.55 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 214 TYR 0.034 0.002 TYR R 540 PHE 0.018 0.002 PHE B 199 TRP 0.016 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8295) covalent geometry : angle 0.57860 (11228) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.56297 ( 2) hydrogen bonds : bond 0.07373 ( 371) hydrogen bonds : angle 4.43957 ( 1038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.189 Fit side-chains REVERT: A 309 GLU cc_start: 0.7850 (pm20) cc_final: 0.7527 (pm20) REVERT: A 356 ARG cc_start: 0.7813 (mtm110) cc_final: 0.7539 (mtm110) REVERT: B 146 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8175 (tp) REVERT: B 262 MET cc_start: 0.7713 (tpp) cc_final: 0.7368 (tpp) REVERT: G 21 MET cc_start: 0.8062 (tpp) cc_final: 0.7627 (tpp) REVERT: R 673 ILE cc_start: 0.8667 (mm) cc_final: 0.8329 (tt) REVERT: R 733 LYS cc_start: 0.8378 (mmpt) cc_final: 0.8085 (mmpt) REVERT: R 775 ASN cc_start: 0.8676 (m-40) cc_final: 0.8368 (m-40) outliers start: 18 outliers final: 6 residues processed: 168 average time/residue: 0.5850 time to fit residues: 103.4024 Evaluate side-chains 161 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 557 LEU Chi-restraints excluded: chain R residue 675 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 42 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 264 ASN A 292 ASN R 720 GLN R 745 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101294 restraints weight = 11595.553| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.13 r_work: 0.3181 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8296 Z= 0.180 Angle : 0.566 7.521 11230 Z= 0.315 Chirality : 0.045 0.177 1269 Planarity : 0.005 0.063 1424 Dihedral : 4.580 30.002 1123 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.49 % Allowed : 11.90 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: 0.49 (0.27), residues: 1019 helix: 1.80 (0.28), residues: 369 sheet: 0.91 (0.33), residues: 240 loop : -1.48 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 214 TYR 0.011 0.001 TYR N 95 PHE 0.018 0.002 PHE B 199 TRP 0.015 0.002 TRP A 234 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8295) covalent geometry : angle 0.56616 (11228) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.32465 ( 2) hydrogen bonds : bond 0.07301 ( 371) hydrogen bonds : angle 4.23857 ( 1038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.219 Fit side-chains REVERT: A 221 MET cc_start: 0.8891 (ttm) cc_final: 0.8533 (ttp) REVERT: A 309 GLU cc_start: 0.7854 (pm20) cc_final: 0.7515 (pm20) REVERT: A 356 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7192 (mtm110) REVERT: B 262 MET cc_start: 0.7742 (tpp) cc_final: 0.7344 (tpp) REVERT: G 21 MET cc_start: 0.8046 (tpp) cc_final: 0.7610 (tpp) REVERT: N 34 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8341 (mmm) REVERT: R 673 ILE cc_start: 0.8679 (mm) cc_final: 0.8356 (tt) REVERT: R 775 ASN cc_start: 0.8698 (m-40) cc_final: 0.8363 (m-40) outliers start: 22 outliers final: 10 residues processed: 168 average time/residue: 0.5280 time to fit residues: 93.6101 Evaluate side-chains 163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 557 LEU Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 682 ARG Chi-restraints excluded: chain R residue 719 THR Chi-restraints excluded: chain R residue 760 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 25 optimal weight: 0.0000 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 264 ASN R 745 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103775 restraints weight = 11808.762| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.17 r_work: 0.3214 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8296 Z= 0.126 Angle : 0.506 6.809 11230 Z= 0.283 Chirality : 0.042 0.179 1269 Planarity : 0.005 0.060 1424 Dihedral : 4.232 27.705 1123 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.27 % Allowed : 15.19 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.27), residues: 1019 helix: 2.08 (0.28), residues: 370 sheet: 0.96 (0.34), residues: 235 loop : -1.35 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 214 TYR 0.011 0.001 TYR B 124 PHE 0.017 0.001 PHE B 199 TRP 0.012 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8295) covalent geometry : angle 0.50627 (11228) SS BOND : bond 0.00124 ( 1) SS BOND : angle 0.38709 ( 2) hydrogen bonds : bond 0.05874 ( 371) hydrogen bonds : angle 3.93223 ( 1038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.314 Fit side-chains REVERT: A 38 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7734 (ttp80) REVERT: A 63 TYR cc_start: 0.6369 (t80) cc_final: 0.5902 (t80) REVERT: A 309 GLU cc_start: 0.7860 (pm20) cc_final: 0.7524 (pm20) REVERT: A 342 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8376 (ttp-170) REVERT: A 356 ARG cc_start: 0.7811 (mtm110) cc_final: 0.7591 (mtm110) REVERT: B 19 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7490 (ttm170) REVERT: B 262 MET cc_start: 0.7650 (tpp) cc_final: 0.7259 (tpp) REVERT: G 21 MET cc_start: 0.8049 (tpp) cc_final: 0.7620 (tpp) REVERT: R 673 ILE cc_start: 0.8650 (mm) cc_final: 0.8330 (tt) REVERT: R 775 ASN cc_start: 0.8649 (m-40) cc_final: 0.8392 (m-40) outliers start: 20 outliers final: 11 residues processed: 166 average time/residue: 0.5196 time to fit residues: 91.4071 Evaluate side-chains 159 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 682 ARG Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain R residue 759 ILE Chi-restraints excluded: chain R residue 760 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 264 ASN A 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102767 restraints weight = 11768.676| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.16 r_work: 0.3204 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8296 Z= 0.145 Angle : 0.515 6.827 11230 Z= 0.288 Chirality : 0.043 0.179 1269 Planarity : 0.005 0.064 1424 Dihedral : 4.218 28.227 1123 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.61 % Allowed : 15.99 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.27), residues: 1019 helix: 2.09 (0.28), residues: 371 sheet: 0.93 (0.34), residues: 237 loop : -1.28 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.011 0.001 TYR N 95 PHE 0.016 0.002 PHE B 199 TRP 0.013 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8295) covalent geometry : angle 0.51481 (11228) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.26413 ( 2) hydrogen bonds : bond 0.06247 ( 371) hydrogen bonds : angle 3.92844 ( 1038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.272 Fit side-chains REVERT: A 38 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7735 (ttp80) REVERT: A 251 SER cc_start: 0.8823 (p) cc_final: 0.8556 (t) REVERT: A 309 GLU cc_start: 0.7832 (pm20) cc_final: 0.7525 (pm20) REVERT: A 342 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8382 (ttp-170) REVERT: A 356 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7614 (mtm110) REVERT: B 19 ARG cc_start: 0.7908 (ttm170) cc_final: 0.7537 (ttm170) REVERT: B 262 MET cc_start: 0.7690 (tpp) cc_final: 0.7300 (tpp) REVERT: G 21 MET cc_start: 0.8059 (tpp) cc_final: 0.7621 (tpp) REVERT: R 673 ILE cc_start: 0.8669 (mm) cc_final: 0.8361 (tt) REVERT: R 717 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7217 (mptt) REVERT: R 775 ASN cc_start: 0.8654 (m-40) cc_final: 0.8387 (m-40) outliers start: 23 outliers final: 12 residues processed: 165 average time/residue: 0.4899 time to fit residues: 85.1805 Evaluate side-chains 168 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 682 ARG Chi-restraints excluded: chain R residue 717 LYS Chi-restraints excluded: chain R residue 759 ILE Chi-restraints excluded: chain R residue 760 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 89 optimal weight: 0.0770 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 264 ASN R 745 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.120703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102113 restraints weight = 11659.802| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.15 r_work: 0.3198 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8296 Z= 0.160 Angle : 0.527 6.729 11230 Z= 0.295 Chirality : 0.043 0.176 1269 Planarity : 0.005 0.058 1424 Dihedral : 4.235 27.645 1123 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.95 % Allowed : 16.21 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.27), residues: 1019 helix: 2.01 (0.28), residues: 373 sheet: 0.95 (0.34), residues: 237 loop : -1.28 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.011 0.001 TYR N 95 PHE 0.017 0.002 PHE B 199 TRP 0.014 0.001 TRP A 234 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8295) covalent geometry : angle 0.52703 (11228) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.25656 ( 2) hydrogen bonds : bond 0.06590 ( 371) hydrogen bonds : angle 3.95481 ( 1038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.182 Fit side-chains REVERT: A 38 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7760 (ttp80) REVERT: A 221 MET cc_start: 0.8877 (ttm) cc_final: 0.8535 (ttp) REVERT: A 251 SER cc_start: 0.8804 (p) cc_final: 0.8526 (t) REVERT: A 274 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7695 (ttmt) REVERT: A 275 SER cc_start: 0.8691 (t) cc_final: 0.8278 (m) REVERT: A 309 GLU cc_start: 0.7835 (pm20) cc_final: 0.7535 (pm20) REVERT: A 342 ARG cc_start: 0.8657 (ttm-80) cc_final: 0.8395 (ttp-170) REVERT: A 347 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: A 356 ARG cc_start: 0.7876 (mtm110) cc_final: 0.7637 (mtm110) REVERT: B 19 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7537 (ttm170) REVERT: G 21 MET cc_start: 0.8040 (tpp) cc_final: 0.7606 (tpp) REVERT: R 673 ILE cc_start: 0.8650 (mm) cc_final: 0.8331 (tt) REVERT: R 717 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7208 (mptt) REVERT: R 775 ASN cc_start: 0.8677 (m-40) cc_final: 0.8374 (m-40) outliers start: 26 outliers final: 17 residues processed: 162 average time/residue: 0.5243 time to fit residues: 89.2745 Evaluate side-chains 168 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 682 ARG Chi-restraints excluded: chain R residue 717 LYS Chi-restraints excluded: chain R residue 719 THR Chi-restraints excluded: chain R residue 760 PHE Chi-restraints excluded: chain R residue 784 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 264 ASN B 75 GLN R 745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.102927 restraints weight = 11729.416| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.16 r_work: 0.3200 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8296 Z= 0.146 Angle : 0.521 6.631 11230 Z= 0.290 Chirality : 0.043 0.171 1269 Planarity : 0.005 0.082 1424 Dihedral : 4.182 27.363 1123 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.06 % Allowed : 17.12 % Favored : 79.82 % 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 aren not related in a simple way. whole: 0.80 (0.27), residues: 1019 helix: 2.09 (0.28), residues: 372 sheet: 0.95 (0.34), residues: 237 loop : -1.25 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 214 TYR 0.011 0.001 TYR N 95 PHE 0.016 0.002 PHE B 199 TRP 0.013 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8295) covalent geometry : angle 0.52126 (11228) SS BOND : bond 0.00093 ( 1) SS BOND : angle 0.26460 ( 2) hydrogen bonds : bond 0.06272 ( 371) hydrogen bonds : angle 3.92214 ( 1038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.223 Fit side-chains REVERT: A 38 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7751 (ttp80) REVERT: A 221 MET cc_start: 0.8872 (ttm) cc_final: 0.8541 (ttp) REVERT: A 251 SER cc_start: 0.8826 (p) cc_final: 0.8525 (t) REVERT: A 274 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7751 (ttmt) REVERT: A 275 SER cc_start: 0.8663 (t) cc_final: 0.8262 (m) REVERT: A 309 GLU cc_start: 0.7841 (pm20) cc_final: 0.7535 (pm20) REVERT: A 356 ARG cc_start: 0.7846 (mtm110) cc_final: 0.7600 (mtm110) REVERT: B 19 ARG cc_start: 0.7895 (ttm170) cc_final: 0.7527 (ttm170) REVERT: G 21 MET cc_start: 0.8017 (tpp) cc_final: 0.7581 (tpp) REVERT: R 643 ARG cc_start: 0.7785 (tmm160) cc_final: 0.7571 (ttp-170) REVERT: R 673 ILE cc_start: 0.8629 (mm) cc_final: 0.8325 (tt) REVERT: R 717 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7231 (mptt) REVERT: R 775 ASN cc_start: 0.8652 (m-40) cc_final: 0.8361 (m110) outliers start: 27 outliers final: 14 residues processed: 161 average time/residue: 0.4728 time to fit residues: 80.6451 Evaluate side-chains 164 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 682 ARG Chi-restraints excluded: chain R residue 717 LYS Chi-restraints excluded: chain R residue 719 THR Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain R residue 760 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 264 ASN B 75 GLN R 745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.120613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102127 restraints weight = 11677.089| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.15 r_work: 0.3197 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8296 Z= 0.158 Angle : 0.533 6.582 11230 Z= 0.298 Chirality : 0.043 0.172 1269 Planarity : 0.005 0.057 1424 Dihedral : 4.198 27.542 1123 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.83 % Allowed : 17.46 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.27), residues: 1019 helix: 2.04 (0.28), residues: 375 sheet: 0.96 (0.34), residues: 235 loop : -1.25 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 214 TYR 0.011 0.001 TYR N 95 PHE 0.017 0.002 PHE B 199 TRP 0.014 0.001 TRP A 234 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8295) covalent geometry : angle 0.53291 (11228) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.24872 ( 2) hydrogen bonds : bond 0.06569 ( 371) hydrogen bonds : angle 3.95481 ( 1038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.210 Fit side-chains REVERT: A 38 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7765 (ttp80) REVERT: A 251 SER cc_start: 0.8809 (p) cc_final: 0.8510 (t) REVERT: A 274 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7789 (ttmt) REVERT: A 275 SER cc_start: 0.8646 (t) cc_final: 0.8252 (m) REVERT: A 309 GLU cc_start: 0.7834 (pm20) cc_final: 0.7536 (pm20) REVERT: A 356 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7623 (mtm110) REVERT: B 19 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7508 (ttm170) REVERT: B 214 ARG cc_start: 0.8786 (ttm-80) cc_final: 0.8479 (ttm170) REVERT: B 234 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: G 21 MET cc_start: 0.8027 (tpp) cc_final: 0.7580 (tpp) REVERT: R 673 ILE cc_start: 0.8645 (mm) cc_final: 0.8343 (tt) REVERT: R 717 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7195 (mptt) REVERT: R 775 ASN cc_start: 0.8668 (m-40) cc_final: 0.8360 (m-40) outliers start: 25 outliers final: 17 residues processed: 158 average time/residue: 0.5124 time to fit residues: 85.4235 Evaluate side-chains 167 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 717 LYS Chi-restraints excluded: chain R residue 719 THR Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain R residue 760 PHE Chi-restraints excluded: chain R residue 784 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 264 ASN B 75 GLN R 745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101846 restraints weight = 11729.625| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.15 r_work: 0.3177 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8296 Z= 0.190 Angle : 0.568 7.018 11230 Z= 0.316 Chirality : 0.044 0.174 1269 Planarity : 0.005 0.056 1424 Dihedral : 4.342 28.543 1123 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.83 % Allowed : 17.69 % Favored : 79.48 % 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 aren not related in a simple way. whole: 0.72 (0.27), residues: 1019 helix: 1.97 (0.28), residues: 375 sheet: 0.82 (0.33), residues: 244 loop : -1.25 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.011 0.001 TYR N 95 PHE 0.018 0.002 PHE B 199 TRP 0.016 0.002 TRP A 234 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8295) covalent geometry : angle 0.56787 (11228) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.23999 ( 2) hydrogen bonds : bond 0.07306 ( 371) hydrogen bonds : angle 4.08754 ( 1038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.291 Fit side-chains REVERT: A 251 SER cc_start: 0.8820 (p) cc_final: 0.8496 (t) REVERT: A 274 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7797 (ttmt) REVERT: A 275 SER cc_start: 0.8679 (t) cc_final: 0.8275 (m) REVERT: A 309 GLU cc_start: 0.7838 (pm20) cc_final: 0.7546 (pm20) REVERT: A 356 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7669 (mtm110) REVERT: B 214 ARG cc_start: 0.8771 (ttm-80) cc_final: 0.8454 (ttm170) REVERT: B 234 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: G 21 MET cc_start: 0.8041 (tpp) cc_final: 0.7579 (tpp) REVERT: R 546 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8406 (ptpp) REVERT: R 673 ILE cc_start: 0.8668 (mm) cc_final: 0.8351 (tt) REVERT: R 676 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7580 (ttpp) REVERT: R 717 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7230 (mptt) REVERT: R 733 LYS cc_start: 0.8340 (mmpt) cc_final: 0.7995 (mmpt) REVERT: R 775 ASN cc_start: 0.8699 (m-40) cc_final: 0.8401 (m-40) outliers start: 25 outliers final: 17 residues processed: 169 average time/residue: 0.5513 time to fit residues: 98.1352 Evaluate side-chains 174 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 717 LYS Chi-restraints excluded: chain R residue 719 THR Chi-restraints excluded: chain R residue 760 PHE Chi-restraints excluded: chain R residue 784 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 264 ASN B 75 GLN R 745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.102544 restraints weight = 11657.731| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.14 r_work: 0.3206 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8296 Z= 0.147 Angle : 0.534 6.603 11230 Z= 0.297 Chirality : 0.043 0.168 1269 Planarity : 0.005 0.057 1424 Dihedral : 4.173 27.087 1123 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.72 % Allowed : 17.91 % Favored : 79.37 % 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 aren not related in a simple way. whole: 0.87 (0.27), residues: 1019 helix: 2.25 (0.28), residues: 369 sheet: 0.94 (0.34), residues: 235 loop : -1.24 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.011 0.001 TYR N 95 PHE 0.015 0.002 PHE B 199 TRP 0.014 0.001 TRP A 277 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8295) covalent geometry : angle 0.53376 (11228) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.30966 ( 2) hydrogen bonds : bond 0.06285 ( 371) hydrogen bonds : angle 3.94944 ( 1038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.207 Fit side-chains REVERT: A 38 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7740 (ttp80) REVERT: A 251 SER cc_start: 0.8829 (p) cc_final: 0.8525 (t) REVERT: A 274 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7813 (ttmt) REVERT: A 275 SER cc_start: 0.8677 (t) cc_final: 0.8276 (m) REVERT: A 309 GLU cc_start: 0.7839 (pm20) cc_final: 0.7537 (pm20) REVERT: A 356 ARG cc_start: 0.7852 (mtm110) cc_final: 0.7640 (mtm110) REVERT: B 214 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8581 (ttm170) REVERT: B 234 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: B 262 MET cc_start: 0.7531 (mmm) cc_final: 0.7231 (tpp) REVERT: G 21 MET cc_start: 0.8028 (tpp) cc_final: 0.7597 (tpp) REVERT: R 546 LYS cc_start: 0.8692 (ptpp) cc_final: 0.8377 (ptpp) REVERT: R 673 ILE cc_start: 0.8628 (mm) cc_final: 0.8392 (tp) REVERT: R 676 LYS cc_start: 0.7988 (ttpp) cc_final: 0.7524 (ttpp) REVERT: R 717 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7218 (mptt) REVERT: R 733 LYS cc_start: 0.8350 (mmpt) cc_final: 0.8021 (mmpt) REVERT: R 775 ASN cc_start: 0.8640 (m-40) cc_final: 0.8402 (m-40) outliers start: 24 outliers final: 17 residues processed: 167 average time/residue: 0.5531 time to fit residues: 97.1504 Evaluate side-chains 175 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 717 LYS Chi-restraints excluded: chain R residue 719 THR Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain R residue 760 PHE Chi-restraints excluded: chain R residue 784 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 264 ASN B 75 GLN R 745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103130 restraints weight = 11650.496| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.14 r_work: 0.3210 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8296 Z= 0.141 Angle : 0.528 7.541 11230 Z= 0.294 Chirality : 0.043 0.168 1269 Planarity : 0.005 0.056 1424 Dihedral : 4.119 26.801 1123 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.61 % Allowed : 18.48 % Favored : 78.91 % 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 aren not related in a simple way. whole: 0.91 (0.27), residues: 1019 helix: 2.31 (0.28), residues: 368 sheet: 0.98 (0.34), residues: 230 loop : -1.23 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.010 0.001 TYR N 95 PHE 0.015 0.002 PHE B 199 TRP 0.016 0.001 TRP A 277 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8295) covalent geometry : angle 0.52769 (11228) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.31180 ( 2) hydrogen bonds : bond 0.06121 ( 371) hydrogen bonds : angle 3.92287 ( 1038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2651.45 seconds wall clock time: 45 minutes 42.93 seconds (2742.93 seconds total)