Starting phenix.real_space_refine on Sat Dec 28 08:10:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydm_33753/12_2024/7ydm_33753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydm_33753/12_2024/7ydm_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_33753/12_2024/7ydm_33753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydm_33753/12_2024/7ydm_33753.map" model { file = "/net/cci-nas-00/data/ceres_data/7ydm_33753/12_2024/7ydm_33753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydm_33753/12_2024/7ydm_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.85, per 1000 atoms: 0.60 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: 1.98 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: 2.34 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: 1.060 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.080 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:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- 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 : 0.917 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: 1.3123 time to fit residues: 247.7868 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 : 1.125 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 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 : 0.972 Fit side-chains REVERT: A 221 MET cc_start: 0.8506 (ttm) cc_final: 0.8167 (ttp) REVERT: A 309 GLU cc_start: 0.7290 (pm20) cc_final: 0.6992 (pm20) REVERT: G 21 MET cc_start: 0.7593 (tpp) cc_final: 0.7226 (tpp) REVERT: R 673 ILE cc_start: 0.8473 (mm) cc_final: 0.8193 (tt) REVERT: R 733 LYS cc_start: 0.8158 (mmpt) cc_final: 0.7905 (mmpt) REVERT: R 775 ASN cc_start: 0.8456 (m-40) cc_final: 0.8127 (m-40) outliers start: 18 outliers final: 7 residues processed: 170 average time/residue: 1.4151 time to fit residues: 253.4708 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 : 0.934 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 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 292 ASN R 720 GLN R 745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1431 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 : 0.536 7.236 11228 Z= 0.298 Chirality : 0.043 0.177 1269 Planarity : 0.005 0.062 1424 Dihedral : 4.445 29.200 1123 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.93 % Allowed : 12.59 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.27), residues: 1019 helix: 1.96 (0.28), residues: 368 sheet: 0.89 (0.33), residues: 240 loop : -1.48 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.011 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 178 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.931 Fit side-chains REVERT: A 309 GLU cc_start: 0.7268 (pm20) cc_final: 0.6954 (pm20) REVERT: B 19 ARG cc_start: 0.7432 (ttm170) cc_final: 0.7041 (ttm170) REVERT: B 72 SER cc_start: 0.8391 (m) cc_final: 0.8190 (m) REVERT: B 146 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7917 (tp) REVERT: G 21 MET cc_start: 0.7600 (tpp) cc_final: 0.7233 (tpp) REVERT: R 673 ILE cc_start: 0.8476 (mm) cc_final: 0.8201 (tt) REVERT: R 775 ASN cc_start: 0.8435 (m-40) cc_final: 0.8165 (m-40) outliers start: 17 outliers final: 8 residues processed: 166 average time/residue: 1.2894 time to fit residues: 226.3021 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 : 0.956 ------------------------------------------------------------------------------- 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 68 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 80 optimal weight: 0.0020 chunk 54 optimal weight: 3.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 0.024 8295 Z= 0.167 Angle : 0.495 6.618 11228 Z= 0.276 Chirality : 0.042 0.176 1269 Planarity : 0.005 0.060 1424 Dihedral : 4.138 27.283 1123 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.15 % Allowed : 14.51 % Favored : 83.33 % 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: 0.83 (0.27), residues: 1019 helix: 2.15 (0.28), residues: 371 sheet: 0.99 (0.34), residues: 235 loop : -1.29 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE B 199 TYR 0.011 0.001 TYR B 124 ARG 0.012 0.000 ARG A 356 *********************** 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 177 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.841 Fit side-chains REVERT: A 24 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.7004 (mmtm) REVERT: A 63 TYR cc_start: 0.5738 (t80) cc_final: 0.5462 (t80) REVERT: A 309 GLU cc_start: 0.7253 (pm20) cc_final: 0.6940 (pm20) REVERT: A 342 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7897 (ttp-170) REVERT: B 19 ARG cc_start: 0.7432 (ttm170) cc_final: 0.7037 (ttm170) REVERT: B 72 SER cc_start: 0.8383 (m) cc_final: 0.8173 (m) REVERT: G 21 MET cc_start: 0.7593 (tpp) cc_final: 0.7232 (tpp) REVERT: N 34 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8147 (mmm) REVERT: R 673 ILE cc_start: 0.8469 (mm) cc_final: 0.8203 (tt) REVERT: R 775 ASN cc_start: 0.8419 (m-40) cc_final: 0.8148 (m110) outliers start: 19 outliers final: 7 residues processed: 167 average time/residue: 1.2584 time to fit residues: 222.4255 Evaluate side-chains 164 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 393 LEU 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 748 LEU Chi-restraints excluded: chain R residue 759 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 B 75 GLN R 745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1776 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= 0.205 Angle : 0.504 6.652 11228 Z= 0.281 Chirality : 0.043 0.178 1269 Planarity : 0.005 0.063 1424 Dihedral : 4.143 27.594 1123 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.49 % Allowed : 15.53 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.27), residues: 1019 helix: 2.11 (0.28), residues: 373 sheet: 1.04 (0.34), residues: 235 loop : -1.25 (0.30), residues: 411 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 0.016 0.002 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.013 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: 22 poor density : 157 time to evaluate : 0.864 Fit side-chains REVERT: A 251 SER cc_start: 0.8702 (p) cc_final: 0.8402 (t) REVERT: A 309 GLU cc_start: 0.7258 (pm20) cc_final: 0.6950 (pm20) REVERT: A 342 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7932 (ttp-170) REVERT: A 356 ARG cc_start: 0.7315 (mtm110) cc_final: 0.6725 (mtm110) REVERT: B 19 ARG cc_start: 0.7469 (ttm170) cc_final: 0.7081 (ttm170) REVERT: B 72 SER cc_start: 0.8383 (m) cc_final: 0.8171 (m) REVERT: B 262 MET cc_start: 0.6749 (tpp) cc_final: 0.6287 (tpp) REVERT: G 21 MET cc_start: 0.7595 (tpp) cc_final: 0.7223 (tpp) REVERT: R 673 ILE cc_start: 0.8486 (mm) cc_final: 0.8213 (tt) REVERT: R 682 ARG cc_start: 0.7095 (tpp80) cc_final: 0.6846 (ttt-90) REVERT: R 717 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7203 (mptt) REVERT: R 775 ASN cc_start: 0.8427 (m-40) cc_final: 0.8162 (m-40) outliers start: 22 outliers final: 13 residues processed: 163 average time/residue: 1.3149 time to fit residues: 226.2175 Evaluate side-chains 167 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 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 748 LEU 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 19 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 B 75 GLN R 745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.005 0.035 8295 Z= 0.306 Angle : 0.557 7.103 11228 Z= 0.311 Chirality : 0.045 0.180 1269 Planarity : 0.005 0.057 1424 Dihedral : 4.359 28.621 1123 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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 (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: 0.70 (0.27), residues: 1019 helix: 2.00 (0.28), residues: 371 sheet: 0.99 (0.34), residues: 235 loop : -1.35 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.009 0.001 HIS A 357 PHE 0.018 0.002 PHE B 199 TYR 0.011 0.001 TYR A 391 ARG 0.008 0.001 ARG B 214 *********************** 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 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.970 Fit side-chains REVERT: A 251 SER cc_start: 0.8701 (p) cc_final: 0.8376 (t) REVERT: A 274 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7458 (ttmt) REVERT: A 309 GLU cc_start: 0.7255 (pm20) cc_final: 0.6970 (pm20) REVERT: B 19 ARG cc_start: 0.7477 (ttm170) cc_final: 0.7082 (ttm170) REVERT: B 72 SER cc_start: 0.8394 (m) cc_final: 0.8187 (m) REVERT: B 262 MET cc_start: 0.6862 (tpp) cc_final: 0.6405 (tpp) REVERT: G 21 MET cc_start: 0.7604 (tpp) cc_final: 0.7218 (tpp) REVERT: R 673 ILE cc_start: 0.8488 (mm) cc_final: 0.8210 (tt) REVERT: R 717 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7143 (mptt) REVERT: R 775 ASN cc_start: 0.8464 (m-40) cc_final: 0.8120 (m-40) outliers start: 23 outliers final: 12 residues processed: 160 average time/residue: 1.3660 time to fit residues: 230.4406 Evaluate side-chains 164 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 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 55 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 745 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8295 Z= 0.228 Angle : 0.522 6.903 11228 Z= 0.291 Chirality : 0.043 0.171 1269 Planarity : 0.005 0.074 1424 Dihedral : 4.218 27.552 1123 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.38 % Allowed : 16.89 % Favored : 80.73 % 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: 2.03 (0.28), residues: 373 sheet: 0.98 (0.34), residues: 235 loop : -1.27 (0.30), residues: 411 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 0.016 0.001 ARG B 214 *********************** 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 169 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.986 Fit side-chains REVERT: A 251 SER cc_start: 0.8692 (p) cc_final: 0.8372 (t) REVERT: A 274 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7525 (ttmt) REVERT: A 275 SER cc_start: 0.8434 (t) cc_final: 0.8028 (m) REVERT: A 309 GLU cc_start: 0.7243 (pm20) cc_final: 0.6958 (pm20) REVERT: A 342 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7948 (ttp-170) REVERT: B 19 ARG cc_start: 0.7462 (ttm170) cc_final: 0.7078 (ttm170) REVERT: B 72 SER cc_start: 0.8368 (m) cc_final: 0.8152 (m) REVERT: G 21 MET cc_start: 0.7591 (tpp) cc_final: 0.7221 (tpp) REVERT: R 673 ILE cc_start: 0.8465 (mm) cc_final: 0.8211 (tt) REVERT: R 717 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7144 (mptt) REVERT: R 775 ASN cc_start: 0.8454 (m-40) cc_final: 0.8184 (m-40) outliers start: 21 outliers final: 12 residues processed: 158 average time/residue: 1.3799 time to fit residues: 230.9964 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 : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 75 GLN R 745 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8295 Z= 0.250 Angle : 0.539 6.705 11228 Z= 0.301 Chirality : 0.044 0.175 1269 Planarity : 0.005 0.056 1424 Dihedral : 4.255 27.928 1123 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.06 % Allowed : 16.89 % Favored : 80.05 % 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: 2.05 (0.28), residues: 370 sheet: 1.01 (0.34), residues: 235 loop : -1.26 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.016 0.002 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.009 0.000 ARG B 214 *********************** 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 185 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.912 Fit side-chains REVERT: A 251 SER cc_start: 0.8696 (p) cc_final: 0.8352 (t) REVERT: A 274 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7555 (ttmt) REVERT: A 275 SER cc_start: 0.8432 (t) cc_final: 0.8030 (m) REVERT: A 309 GLU cc_start: 0.7239 (pm20) cc_final: 0.6955 (pm20) REVERT: B 72 SER cc_start: 0.8378 (m) cc_final: 0.8167 (m) REVERT: B 214 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7782 (ttm170) REVERT: B 234 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: G 21 MET cc_start: 0.7588 (tpp) cc_final: 0.7212 (tpp) REVERT: N 34 MET cc_start: 0.8095 (mmt) cc_final: 0.7423 (mmm) REVERT: R 546 LYS cc_start: 0.8408 (ptpp) cc_final: 0.8090 (ptpp) REVERT: R 552 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7075 (mtt-85) REVERT: R 673 ILE cc_start: 0.8474 (mm) cc_final: 0.8208 (tt) REVERT: R 717 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7143 (mptt) REVERT: R 733 LYS cc_start: 0.8003 (mmpt) cc_final: 0.7755 (mmpt) REVERT: R 775 ASN cc_start: 0.8478 (m-40) cc_final: 0.8179 (m-40) outliers start: 27 outliers final: 16 residues processed: 169 average time/residue: 1.3909 time to fit residues: 247.5120 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 : 0.986 ------------------------------------------------------------------------------- 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 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 234 PHE 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 552 ARG 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 0.1980 chunk 57 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 R 745 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8295 Z= 0.159 Angle : 0.487 6.348 11228 Z= 0.272 Chirality : 0.042 0.162 1269 Planarity : 0.004 0.056 1424 Dihedral : 3.965 25.286 1123 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.81 % Allowed : 18.48 % 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 (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: 2.35 (0.28), residues: 367 sheet: 1.03 (0.33), residues: 235 loop : -1.17 (0.30), residues: 417 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 B 124 ARG 0.009 0.000 ARG B 214 *********************** 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 177 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.857 Fit side-chains REVERT: A 251 SER cc_start: 0.8678 (p) cc_final: 0.8398 (t) REVERT: A 275 SER cc_start: 0.8387 (t) cc_final: 0.7970 (m) REVERT: A 309 GLU cc_start: 0.7236 (pm20) cc_final: 0.6944 (pm20) REVERT: A 342 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7909 (ttp-170) REVERT: B 19 ARG cc_start: 0.7430 (ttm170) cc_final: 0.7053 (ttm170) REVERT: B 72 SER cc_start: 0.8344 (m) cc_final: 0.8137 (m) REVERT: B 214 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7842 (ttm170) REVERT: B 234 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: G 21 MET cc_start: 0.7582 (tpp) cc_final: 0.7223 (tpp) REVERT: R 552 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6782 (mtt-85) REVERT: R 676 LYS cc_start: 0.7368 (ttpp) cc_final: 0.6972 (ttpp) REVERT: R 733 LYS cc_start: 0.7997 (mmpt) cc_final: 0.7724 (mmpt) REVERT: R 775 ASN cc_start: 0.8400 (m-40) cc_final: 0.8137 (m110) outliers start: 16 outliers final: 11 residues processed: 168 average time/residue: 1.3682 time to fit residues: 242.7325 Evaluate side-chains 172 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 234 PHE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 552 ARG 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 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 R 745 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8295 Z= 0.220 Angle : 0.518 6.166 11228 Z= 0.289 Chirality : 0.043 0.166 1269 Planarity : 0.004 0.055 1424 Dihedral : 4.082 26.639 1123 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.93 % Allowed : 18.71 % 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 (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: 0.92 (0.27), residues: 1019 helix: 2.26 (0.28), residues: 369 sheet: 1.04 (0.34), residues: 230 loop : -1.21 (0.30), residues: 420 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 0.016 0.002 PHE B 199 TYR 0.010 0.001 TYR N 95 ARG 0.009 0.000 ARG A 356 ********************** 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 169 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.900 Fit side-chains REVERT: A 251 SER cc_start: 0.8689 (p) cc_final: 0.8376 (t) REVERT: A 275 SER cc_start: 0.8362 (t) cc_final: 0.7938 (m) REVERT: A 309 GLU cc_start: 0.7244 (pm20) cc_final: 0.6947 (pm20) REVERT: A 349 SER cc_start: 0.8391 (p) cc_final: 0.7950 (p) REVERT: B 19 ARG cc_start: 0.7474 (ttm170) cc_final: 0.7102 (ttm170) REVERT: B 72 SER cc_start: 0.8369 (m) cc_final: 0.8159 (m) REVERT: B 214 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7865 (ttm170) REVERT: B 234 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: G 21 MET cc_start: 0.7579 (tpp) cc_final: 0.7216 (tpp) REVERT: N 34 MET cc_start: 0.7986 (mmt) cc_final: 0.7528 (mmm) REVERT: R 552 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7010 (mtt-85) REVERT: R 676 LYS cc_start: 0.7382 (ttpp) cc_final: 0.6983 (ttpp) REVERT: R 733 LYS cc_start: 0.8005 (mmpt) cc_final: 0.7730 (mmpt) REVERT: R 775 ASN cc_start: 0.8430 (m-40) cc_final: 0.8128 (m110) outliers start: 17 outliers final: 12 residues processed: 163 average time/residue: 1.3857 time to fit residues: 238.1946 Evaluate side-chains 166 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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 234 PHE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain R residue 552 ARG Chi-restraints excluded: chain R residue 675 SER Chi-restraints excluded: chain R residue 719 THR Chi-restraints excluded: chain R residue 724 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.0010 chunk 79 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 0.0670 chunk 57 optimal weight: 4.9990 overall best weight: 0.2324 ------------------------------------------------------------------------------- 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 R 745 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.125092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106645 restraints weight = 11566.262| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.13 r_work: 0.3277 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8295 Z= 0.135 Angle : 0.474 7.631 11228 Z= 0.263 Chirality : 0.041 0.159 1269 Planarity : 0.004 0.056 1424 Dihedral : 3.799 23.031 1123 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.59 % Allowed : 19.61 % Favored : 78.80 % 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: 2.49 (0.28), residues: 368 sheet: 1.06 (0.33), residues: 238 loop : -1.17 (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 0.013 0.001 PHE B 199 TYR 0.009 0.001 TYR B 124 ARG 0.011 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3947.85 seconds wall clock time: 71 minutes 12.32 seconds (4272.32 seconds total)