Starting phenix.real_space_refine on Wed Feb 12 16:23:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydm_33753/02_2025/7ydm_33753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydm_33753/02_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_33753/02_2025/7ydm_33753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydm_33753/02_2025/7ydm_33753.map" model { file = "/net/cci-nas-00/data/ceres_data/7ydm_33753/02_2025/7ydm_33753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydm_33753/02_2025/7ydm_33753.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.63, per 1000 atoms: 0.57 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: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.90 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: 2.27 Time building geometry restraints manager: 2.29 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: 0.960 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.240 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- 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 8295 Z= 0.446 Angle : 0.725 9.039 11228 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (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 TRP 0.022 0.002 TRP A 234 HIS 0.014 0.002 HIS A 357 PHE 0.025 0.003 PHE N 108 TYR 0.013 0.002 TYR N 95 ARG 0.007 0.000 ARG A 336 *********************** 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 : 0.840 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: 1.3318 time to fit residues: 251.5626 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 : 0.939 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.121007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102585 restraints weight = 11544.460| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.13 r_work: 0.3198 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8295 Z= 0.231 Angle : 0.570 7.615 11228 Z= 0.317 Chirality : 0.044 0.184 1269 Planarity : 0.005 0.073 1424 Dihedral : 4.689 29.836 1125 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.04 % Allowed : 8.50 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 1019 helix: 1.64 (0.28), residues: 369 sheet: 0.85 (0.33), residues: 246 loop : -1.54 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.018 0.002 PHE B 199 TYR 0.035 0.002 TYR R 540 ARG 0.011 0.000 ARG B 214 *********************** 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 181 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.856 Fit side-chains REVERT: A 221 MET cc_start: 0.8865 (ttm) cc_final: 0.8553 (ttp) REVERT: A 309 GLU cc_start: 0.7854 (pm20) cc_final: 0.7527 (pm20) REVERT: A 356 ARG cc_start: 0.7793 (mtm110) cc_final: 0.7520 (mtm110) REVERT: G 21 MET cc_start: 0.8045 (tpp) cc_final: 0.7612 (tpp) REVERT: R 673 ILE cc_start: 0.8655 (mm) cc_final: 0.8318 (tt) REVERT: R 733 LYS cc_start: 0.8387 (mmpt) cc_final: 0.8088 (mmpt) REVERT: R 775 ASN cc_start: 0.8692 (m-40) cc_final: 0.8368 (m-40) outliers start: 18 outliers final: 7 residues processed: 170 average time/residue: 1.3764 time to fit residues: 247.1363 Evaluate side-chains 162 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 R 720 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 = 0.3587 r_free = 0.3587 target = 0.121201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102719 restraints weight = 11687.904| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.15 r_work: 0.3203 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8295 Z= 0.221 Angle : 0.534 7.183 11228 Z= 0.297 Chirality : 0.043 0.173 1269 Planarity : 0.005 0.062 1424 Dihedral : 4.429 29.153 1123 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.93 % Allowed : 12.81 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 1019 helix: 1.98 (0.28), residues: 368 sheet: 0.90 (0.33), residues: 240 loop : -1.47 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.017 0.002 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.012 0.000 ARG B 214 *********************** 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 180 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.945 Fit side-chains REVERT: A 309 GLU cc_start: 0.7855 (pm20) cc_final: 0.7517 (pm20) REVERT: B 19 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7470 (ttm170) REVERT: B 133 VAL cc_start: 0.8413 (m) cc_final: 0.8211 (t) REVERT: B 146 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8069 (tp) REVERT: G 21 MET cc_start: 0.8046 (tpp) cc_final: 0.7610 (tpp) REVERT: R 673 ILE cc_start: 0.8667 (mm) cc_final: 0.8337 (tt) REVERT: R 775 ASN cc_start: 0.8655 (m-40) cc_final: 0.8398 (m-40) outliers start: 17 outliers final: 8 residues processed: 168 average time/residue: 1.3007 time to fit residues: 230.9268 Evaluate side-chains 158 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 548 THR Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 682 ARG 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 18 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 0.0670 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 387 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 = 0.3594 r_free = 0.3594 target = 0.121556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103088 restraints weight = 11554.457| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.14 r_work: 0.3211 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8295 Z= 0.199 Angle : 0.511 6.733 11228 Z= 0.285 Chirality : 0.043 0.180 1269 Planarity : 0.005 0.060 1424 Dihedral : 4.227 28.144 1123 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.72 % Allowed : 14.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 1019 helix: 2.10 (0.28), residues: 370 sheet: 1.01 (0.34), residues: 230 loop : -1.33 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.002 PHE B 199 TYR 0.011 0.001 TYR B 124 ARG 0.012 0.000 ARG B 214 *********************** 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 178 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.900 Fit side-chains REVERT: A 63 TYR cc_start: 0.6374 (t80) cc_final: 0.5911 (t80) REVERT: A 309 GLU cc_start: 0.7825 (pm20) cc_final: 0.7489 (pm20) REVERT: A 342 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.8382 (ttp-170) REVERT: A 356 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7539 (mtm110) REVERT: B 19 ARG cc_start: 0.7903 (ttm170) cc_final: 0.7528 (ttm170) REVERT: G 21 MET cc_start: 0.8056 (tpp) cc_final: 0.7620 (tpp) REVERT: R 673 ILE cc_start: 0.8662 (mm) cc_final: 0.8346 (tt) REVERT: R 775 ASN cc_start: 0.8653 (m-40) cc_final: 0.8397 (m-40) outliers start: 24 outliers final: 12 residues processed: 164 average time/residue: 1.3192 time to fit residues: 228.6674 Evaluate side-chains 164 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 393 LEU 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 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 60 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 0.0060 chunk 35 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102862 restraints weight = 11591.851| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.15 r_work: 0.3210 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8295 Z= 0.211 Angle : 0.512 6.818 11228 Z= 0.285 Chirality : 0.043 0.180 1269 Planarity : 0.005 0.064 1424 Dihedral : 4.199 27.887 1123 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.95 % Allowed : 15.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 1019 helix: 2.10 (0.28), residues: 371 sheet: 0.91 (0.34), residues: 234 loop : -1.27 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.002 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.014 0.000 ARG B 214 *********************** 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 179 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.928 Fit side-chains REVERT: A 221 MET cc_start: 0.8824 (ttm) cc_final: 0.8467 (ttp) REVERT: A 251 SER cc_start: 0.8830 (p) cc_final: 0.8557 (t) REVERT: A 309 GLU cc_start: 0.7826 (pm20) cc_final: 0.7521 (pm20) REVERT: A 342 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8392 (ttp-170) REVERT: A 356 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7570 (mtm110) REVERT: B 19 ARG cc_start: 0.7877 (ttm170) cc_final: 0.7499 (ttm170) REVERT: G 21 MET cc_start: 0.8030 (tpp) cc_final: 0.7606 (tpp) REVERT: N 34 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7879 (mmm) REVERT: R 673 ILE cc_start: 0.8672 (mm) cc_final: 0.8365 (tt) REVERT: R 717 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7254 (mptt) REVERT: R 775 ASN cc_start: 0.8644 (m-40) cc_final: 0.8381 (m-40) outliers start: 26 outliers final: 15 residues processed: 162 average time/residue: 1.2920 time to fit residues: 221.1148 Evaluate side-chains 168 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 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 146 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain N residue 30 SER 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 675 SER Chi-restraints excluded: chain R residue 682 ARG Chi-restraints excluded: chain R residue 717 LYS Chi-restraints excluded: chain R residue 748 LEU 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 49 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101152 restraints weight = 11634.914| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.15 r_work: 0.3177 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8295 Z= 0.288 Angle : 0.558 7.447 11228 Z= 0.310 Chirality : 0.044 0.181 1269 Planarity : 0.005 0.059 1424 Dihedral : 4.356 28.851 1123 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.38 % Allowed : 16.67 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 1019 helix: 1.95 (0.28), residues: 371 sheet: 0.99 (0.34), residues: 230 loop : -1.37 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.018 0.002 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.009 0.000 ARG B 219 *********************** 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 170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.903 Fit side-chains REVERT: A 251 SER cc_start: 0.8817 (p) cc_final: 0.8528 (t) REVERT: A 274 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7713 (ttmt) REVERT: A 275 SER cc_start: 0.8726 (t) cc_final: 0.8316 (m) REVERT: A 309 GLU cc_start: 0.7831 (pm20) cc_final: 0.7531 (pm20) REVERT: A 356 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7624 (mtm110) REVERT: B 19 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7527 (ttm170) REVERT: B 214 ARG cc_start: 0.8835 (ttm-80) cc_final: 0.8541 (ttm170) REVERT: G 21 MET cc_start: 0.8052 (tpp) cc_final: 0.7602 (tpp) REVERT: R 643 ARG cc_start: 0.7890 (tmm160) cc_final: 0.7637 (ttt180) REVERT: R 673 ILE cc_start: 0.8671 (mm) cc_final: 0.8346 (tt) REVERT: R 717 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7238 (mptt) REVERT: R 775 ASN cc_start: 0.8689 (m-40) cc_final: 0.8362 (m-40) outliers start: 21 outliers final: 12 residues processed: 158 average time/residue: 1.3865 time to fit residues: 231.6950 Evaluate side-chains 162 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 146 LEU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 0.0050 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102531 restraints weight = 11685.110| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.14 r_work: 0.3197 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8295 Z= 0.227 Angle : 0.519 7.604 11228 Z= 0.289 Chirality : 0.043 0.171 1269 Planarity : 0.005 0.058 1424 Dihedral : 4.209 27.610 1123 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.06 % Allowed : 16.33 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 1019 helix: 2.16 (0.28), residues: 366 sheet: 0.97 (0.34), residues: 230 loop : -1.30 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.002 PHE B 199 TYR 0.011 0.001 TYR B 124 ARG 0.008 0.000 ARG B 219 *********************** 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 175 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.864 Fit side-chains REVERT: A 221 MET cc_start: 0.8857 (ttm) cc_final: 0.8529 (ttp) REVERT: A 251 SER cc_start: 0.8835 (p) cc_final: 0.8535 (t) REVERT: A 274 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7762 (ttmt) REVERT: A 275 SER cc_start: 0.8685 (t) cc_final: 0.8280 (m) REVERT: A 309 GLU cc_start: 0.7837 (pm20) cc_final: 0.7533 (pm20) REVERT: A 356 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7580 (mtm110) REVERT: G 21 MET cc_start: 0.8035 (tpp) cc_final: 0.7597 (tpp) REVERT: N 34 MET cc_start: 0.8292 (mmt) cc_final: 0.7603 (mmm) REVERT: R 673 ILE cc_start: 0.8643 (mm) cc_final: 0.8343 (tt) REVERT: R 717 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7230 (mptt) REVERT: R 775 ASN cc_start: 0.8673 (m-40) cc_final: 0.8416 (m-40) outliers start: 27 outliers final: 15 residues processed: 160 average time/residue: 1.3512 time to fit residues: 228.3857 Evaluate side-chains 168 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 146 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 315 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.0000 chunk 79 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.123777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105264 restraints weight = 11772.387| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.17 r_work: 0.3249 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8295 Z= 0.143 Angle : 0.471 8.520 11228 Z= 0.262 Chirality : 0.041 0.162 1269 Planarity : 0.004 0.057 1424 Dihedral : 3.884 25.413 1123 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.04 % Allowed : 18.03 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 1019 helix: 2.40 (0.28), residues: 368 sheet: 0.98 (0.33), residues: 235 loop : -1.19 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.001 PHE B 199 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG B 219 *********************** 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 168 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.984 Fit side-chains REVERT: A 274 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7767 (ttmt) REVERT: A 309 GLU cc_start: 0.7828 (pm20) cc_final: 0.7512 (pm20) REVERT: A 342 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.8375 (ttp-170) REVERT: B 234 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: G 21 MET cc_start: 0.8012 (tpp) cc_final: 0.7584 (tpp) REVERT: N 60 TYR cc_start: 0.8657 (m-80) cc_final: 0.8137 (m-80) REVERT: R 673 ILE cc_start: 0.8606 (mm) cc_final: 0.8381 (tp) REVERT: R 775 ASN cc_start: 0.8592 (m-40) cc_final: 0.8212 (m-40) outliers start: 18 outliers final: 8 residues processed: 158 average time/residue: 1.3292 time to fit residues: 222.3020 Evaluate side-chains 157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 234 PHE Chi-restraints excluded: chain N residue 49 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 719 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.103814 restraints weight = 11828.127| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.15 r_work: 0.3222 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8295 Z= 0.184 Angle : 0.494 8.741 11228 Z= 0.275 Chirality : 0.042 0.164 1269 Planarity : 0.004 0.057 1424 Dihedral : 3.974 25.638 1123 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.47 % Allowed : 18.93 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 1019 helix: 2.42 (0.28), residues: 368 sheet: 0.95 (0.34), residues: 232 loop : -1.10 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 277 HIS 0.008 0.001 HIS A 357 PHE 0.015 0.001 PHE B 199 TYR 0.010 0.001 TYR B 124 ARG 0.008 0.000 ARG B 219 *********************** 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 164 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 251 SER cc_start: 0.8824 (p) cc_final: 0.8534 (t) REVERT: A 275 SER cc_start: 0.8641 (t) cc_final: 0.8240 (m) REVERT: A 309 GLU cc_start: 0.7835 (pm20) cc_final: 0.7519 (pm20) REVERT: A 342 ARG cc_start: 0.8638 (ttm-80) cc_final: 0.8401 (ttp-170) REVERT: B 19 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7523 (ttm170) REVERT: B 234 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: G 21 MET cc_start: 0.8039 (tpp) cc_final: 0.7607 (tpp) REVERT: R 673 ILE cc_start: 0.8638 (mm) cc_final: 0.8398 (tp) REVERT: R 716 TRP cc_start: 0.8129 (t60) cc_final: 0.7743 (t-100) REVERT: R 775 ASN cc_start: 0.8611 (m-40) cc_final: 0.8358 (m110) outliers start: 13 outliers final: 10 residues processed: 157 average time/residue: 1.2655 time to fit residues: 210.2015 Evaluate side-chains 161 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 719 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 0.5980 chunk 90 optimal weight: 0.2980 chunk 30 optimal weight: 0.1980 chunk 74 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106579 restraints weight = 11634.564| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.15 r_work: 0.3269 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8295 Z= 0.133 Angle : 0.465 9.296 11228 Z= 0.257 Chirality : 0.041 0.158 1269 Planarity : 0.004 0.057 1424 Dihedral : 3.752 23.073 1123 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.59 % Allowed : 19.27 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1019 helix: 2.60 (0.28), residues: 368 sheet: 0.99 (0.33), residues: 238 loop : -1.12 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 199 TYR 0.009 0.001 TYR B 124 ARG 0.008 0.000 ARG B 219 ********************** 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 165 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7847 (ttmt) REVERT: A 342 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.8342 (ttp-170) REVERT: A 356 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7663 (mtm110) REVERT: B 19 ARG cc_start: 0.7874 (ttm170) cc_final: 0.7498 (ttm170) REVERT: B 234 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: B 262 MET cc_start: 0.6994 (mmm) cc_final: 0.6727 (tpp) REVERT: G 21 MET cc_start: 0.8023 (tpp) cc_final: 0.7609 (tpp) REVERT: G 46 LYS cc_start: 0.8414 (mtmm) cc_final: 0.8166 (mtmm) REVERT: N 60 TYR cc_start: 0.8589 (m-80) cc_final: 0.8221 (m-80) REVERT: R 673 ILE cc_start: 0.8599 (mm) cc_final: 0.8368 (tp) REVERT: R 716 TRP cc_start: 0.8081 (t60) cc_final: 0.7688 (t-100) REVERT: R 775 ASN cc_start: 0.8562 (m-40) cc_final: 0.8204 (m-40) outliers start: 14 outliers final: 9 residues processed: 156 average time/residue: 1.3172 time to fit residues: 216.9362 Evaluate side-chains 156 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 234 PHE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 719 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 97 optimal weight: 0.0470 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103548 restraints weight = 11731.587| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.16 r_work: 0.3216 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8295 Z= 0.203 Angle : 0.505 8.662 11228 Z= 0.280 Chirality : 0.042 0.164 1269 Planarity : 0.004 0.056 1424 Dihedral : 3.968 25.380 1123 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.81 % Allowed : 19.61 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1019 helix: 2.52 (0.28), residues: 368 sheet: 0.96 (0.33), residues: 235 loop : -1.11 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.002 PHE B 199 TYR 0.010 0.001 TYR N 95 ARG 0.007 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6184.86 seconds wall clock time: 109 minutes 36.90 seconds (6576.90 seconds total)