Starting phenix.real_space_refine on Fri Aug 22 21:20:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydp_33755/08_2025/7ydp_33755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydp_33755/08_2025/7ydp_33755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ydp_33755/08_2025/7ydp_33755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydp_33755/08_2025/7ydp_33755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ydp_33755/08_2025/7ydp_33755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydp_33755/08_2025/7ydp_33755.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 5100 2.51 5 N 1392 2.21 5 O 1481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8028 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2106 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1922 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} 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} Time building chain proxies: 1.94, per 1000 atoms: 0.24 Number of scatterers: 8028 At special positions: 0 Unit cell: (78.1, 97.9, 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 1481 8.00 N 1392 7.00 C 5100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 612 " - pdb=" SG CYS R 684 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 324.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1910 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 41.1% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'R' and resid 532 through 537 Processing helix chain 'R' and resid 544 through 572 removed outlier: 3.511A pdb=" N THR R 548 " --> pdb=" O ASP R 544 " (cutoff:3.500A) Processing helix chain 'R' and resid 577 through 601 removed outlier: 3.640A pdb=" N THR R 581 " --> pdb=" O GLY R 577 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE R 601 " --> pdb=" O PHE R 597 " (cutoff:3.500A) Processing helix chain 'R' and resid 609 through 642 removed outlier: 3.907A pdb=" N SER R 631 " --> pdb=" O PHE R 627 " (cutoff:3.500A) Processing helix chain 'R' and resid 652 through 669 Proline residue: R 663 - end of helix Processing helix chain 'R' and resid 688 through 695 removed outlier: 6.082A pdb=" N LEU R 693 " --> pdb=" O GLN R 690 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP R 694 " --> pdb=" O GLY R 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER R 695 " --> pdb=" O PHE R 692 " (cutoff:3.500A) Processing helix chain 'R' and resid 697 through 726 removed outlier: 3.587A pdb=" N SER R 723 " --> pdb=" O THR R 719 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU R 724 " --> pdb=" O GLN R 720 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN R 726 " --> pdb=" O PHE R 722 " (cutoff:3.500A) Processing helix chain 'R' and resid 730 through 749 Processing helix chain 'R' and resid 751 through 758 Processing helix chain 'R' and resid 764 through 775 Processing helix chain 'R' and resid 777 through 786 Processing helix chain 'R' and resid 790 through 802 removed outlier: 3.909A pdb=" N GLU R 795 " --> pdb=" O LYS R 791 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU R 796 " --> pdb=" O LYS R 792 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG R 798 " --> pdb=" O ARG R 794 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS R 799 " --> pdb=" O GLU R 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.748A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 42 removed outlier: 3.860A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.504A pdb=" N GLU C 47 " --> pdb=" O HIS C 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 40 removed outlier: 4.362A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.528A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.745A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.759A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.576A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.966A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.812A pdb=" N ASN D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.068A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.695A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.622A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.019A pdb=" N GLY D 10 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D 50 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 59 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.296A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 removed outlier: 7.160A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.794A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 7.197A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.117A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.695A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.962A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.77 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: 2557 1.34 - 1.45: 1270 1.45 - 1.57: 4292 1.57 - 1.69: 0 1.69 - 1.81: 73 Bond restraints: 8192 Sorted by residual: bond pdb=" C ARG D 98 " pdb=" N CYS D 99 " ideal model delta sigma weight residual 1.340 1.234 0.106 5.87e-02 2.90e+02 3.28e+00 bond pdb=" CA SER B 67 " pdb=" C SER B 67 " ideal model delta sigma weight residual 1.524 1.501 0.023 1.59e-02 3.96e+03 2.10e+00 bond pdb=" CB TRP D 36 " pdb=" CG TRP D 36 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.64e+00 bond pdb=" CG LEU R 619 " pdb=" CD2 LEU R 619 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CA ASN B 313 " pdb=" CB ASN B 313 " ideal model delta sigma weight residual 1.538 1.525 0.013 1.22e-02 6.72e+03 1.10e+00 ... (remaining 8187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 10580 1.56 - 3.12: 438 3.12 - 4.68: 57 4.68 - 6.24: 16 6.24 - 7.80: 5 Bond angle restraints: 11096 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 112.43 108.48 3.95 9.20e-01 1.18e+00 1.84e+01 angle pdb=" N GLY R 600 " pdb=" CA GLY R 600 " pdb=" C GLY R 600 " ideal model delta sigma weight residual 115.80 123.07 -7.27 1.74e+00 3.30e-01 1.74e+01 angle pdb=" C TYR B 105 " pdb=" N ALA B 106 " pdb=" CA ALA B 106 " ideal model delta sigma weight residual 120.68 125.97 -5.29 1.52e+00 4.33e-01 1.21e+01 angle pdb=" CA SER B 67 " pdb=" C SER B 67 " pdb=" N ARG B 68 " ideal model delta sigma weight residual 117.92 113.86 4.06 1.35e+00 5.49e-01 9.05e+00 angle pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " pdb=" CG TYR B 105 " ideal model delta sigma weight residual 113.90 119.07 -5.17 1.80e+00 3.09e-01 8.26e+00 ... (remaining 11091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 4434 16.67 - 33.34: 343 33.34 - 50.01: 60 50.01 - 66.69: 9 66.69 - 83.36: 6 Dihedral angle restraints: 4852 sinusoidal: 1893 harmonic: 2959 Sorted by residual: dihedral pdb=" CA PHE D 108 " pdb=" C PHE D 108 " pdb=" N ASP D 109 " pdb=" CA ASP D 109 " ideal model delta harmonic sigma weight residual 180.00 154.10 25.90 0 5.00e+00 4.00e-02 2.68e+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 -127.49 41.49 1 1.00e+01 1.00e-02 2.41e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual -86.00 -45.94 -40.06 1 1.00e+01 1.00e-02 2.25e+01 ... (remaining 4849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 747 0.035 - 0.071: 340 0.071 - 0.106: 120 0.106 - 0.142: 43 0.142 - 0.177: 5 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA GLN R 745 " pdb=" N GLN R 745 " pdb=" C GLN R 745 " pdb=" CB GLN R 745 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CG LEU R 598 " pdb=" CB LEU R 598 " pdb=" CD1 LEU R 598 " pdb=" CD2 LEU R 598 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 1252 not shown) Planarity restraints: 1411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 101 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO D 102 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 680 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO R 681 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 681 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 681 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 40 " -0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO D 41 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 41 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 41 " -0.026 5.00e-02 4.00e+02 ... (remaining 1408 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 156 2.68 - 3.23: 7593 3.23 - 3.79: 11885 3.79 - 4.34: 15680 4.34 - 4.90: 26132 Nonbonded interactions: 61446 Sorted by model distance: nonbonded pdb=" OE2 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.123 3.040 nonbonded pdb=" OD1 ASP B 212 " pdb=" N VAL B 213 " model vdw 2.172 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.237 3.040 nonbonded pdb=" OE1 GLU B 130 " pdb=" NH2 ARG B 134 " model vdw 2.250 3.120 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.258 3.040 ... (remaining 61441 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 8194 Z= 0.212 Angle : 0.734 7.803 11100 Z= 0.432 Chirality : 0.047 0.177 1255 Planarity : 0.005 0.061 1411 Dihedral : 12.575 83.357 2936 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.25), residues: 1008 helix: 0.57 (0.27), residues: 362 sheet: -0.16 (0.35), residues: 182 loop : -2.25 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 48 TYR 0.022 0.002 TYR B 124 PHE 0.030 0.003 PHE B 151 TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS R 583 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8192) covalent geometry : angle 0.73289 (11096) SS BOND : bond 0.00723 ( 2) SS BOND : angle 2.08908 ( 4) hydrogen bonds : bond 0.13298 ( 382) hydrogen bonds : angle 5.51256 ( 1047) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.5104 (mmp) cc_final: 0.4792 (mmt) REVERT: B 59 TYR cc_start: 0.4344 (p90) cc_final: 0.3898 (p90) REVERT: B 102 THR cc_start: 0.6778 (t) cc_final: 0.5466 (m) REVERT: B 217 MET cc_start: 0.6210 (tmm) cc_final: 0.5989 (tmm) REVERT: B 297 TRP cc_start: 0.7084 (m100) cc_final: 0.6781 (m100) REVERT: B 304 ARG cc_start: 0.6952 (ttp-170) cc_final: 0.6457 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0906 time to fit residues: 17.7416 Evaluate side-chains 136 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 576 GLN ** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.185860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.161332 restraints weight = 11208.751| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.31 r_work: 0.4052 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8194 Z= 0.143 Angle : 0.620 10.633 11100 Z= 0.336 Chirality : 0.043 0.149 1255 Planarity : 0.005 0.055 1411 Dihedral : 5.310 23.189 1112 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.81 % Allowed : 7.29 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.26), residues: 1008 helix: 0.98 (0.28), residues: 372 sheet: 0.05 (0.33), residues: 208 loop : -2.03 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.018 0.002 TYR B 124 PHE 0.019 0.002 PHE A 212 TRP 0.022 0.002 TRP B 297 HIS 0.006 0.001 HIS R 583 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8192) covalent geometry : angle 0.62019 (11096) SS BOND : bond 0.00272 ( 2) SS BOND : angle 0.55083 ( 4) hydrogen bonds : bond 0.05733 ( 382) hydrogen bonds : angle 4.68498 ( 1047) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 576 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: R 783 TYR cc_start: 0.6800 (t80) cc_final: 0.5924 (t80) REVERT: A 350 THR cc_start: 0.7919 (t) cc_final: 0.7540 (t) REVERT: A 386 MET cc_start: 0.6102 (mmp) cc_final: 0.5564 (mmt) REVERT: B 45 MET cc_start: 0.7664 (mtm) cc_final: 0.6951 (ptp) REVERT: B 59 TYR cc_start: 0.4627 (p90) cc_final: 0.4050 (p90) REVERT: B 100 VAL cc_start: 0.6910 (OUTLIER) cc_final: 0.6622 (p) REVERT: B 102 THR cc_start: 0.6882 (t) cc_final: 0.5536 (m) REVERT: B 186 ASP cc_start: 0.4610 (p0) cc_final: 0.4365 (p0) REVERT: B 217 MET cc_start: 0.6748 (tmm) cc_final: 0.6371 (tmm) REVERT: B 219 ARG cc_start: 0.7395 (mtp85) cc_final: 0.7176 (mtp85) REVERT: B 297 TRP cc_start: 0.7420 (m100) cc_final: 0.6428 (m100) outliers start: 7 outliers final: 4 residues processed: 136 average time/residue: 0.0852 time to fit residues: 15.6631 Evaluate side-chains 131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 559 LEU Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.183455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.158889 restraints weight = 11166.210| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.30 r_work: 0.4002 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 8194 Z= 0.195 Angle : 0.634 10.516 11100 Z= 0.347 Chirality : 0.045 0.151 1255 Planarity : 0.005 0.052 1411 Dihedral : 5.314 23.037 1112 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.85 % Allowed : 9.26 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.26), residues: 1008 helix: 1.04 (0.28), residues: 373 sheet: 0.06 (0.33), residues: 208 loop : -2.00 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.020 0.002 TYR B 124 PHE 0.025 0.002 PHE B 199 TRP 0.015 0.002 TRP B 169 HIS 0.009 0.002 HIS R 786 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 8192) covalent geometry : angle 0.63446 (11096) SS BOND : bond 0.00355 ( 2) SS BOND : angle 0.15414 ( 4) hydrogen bonds : bond 0.06125 ( 382) hydrogen bonds : angle 4.67865 ( 1047) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 576 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7444 (mp-120) REVERT: R 729 MET cc_start: 0.1717 (ttp) cc_final: 0.1480 (ttp) REVERT: R 745 GLN cc_start: 0.7121 (mp10) cc_final: 0.6851 (mp10) REVERT: R 783 TYR cc_start: 0.7003 (t80) cc_final: 0.6249 (t80) REVERT: A 60 MET cc_start: 0.5214 (OUTLIER) cc_final: 0.4958 (mtm) REVERT: A 221 MET cc_start: 0.7459 (mtt) cc_final: 0.7115 (mtp) REVERT: A 350 THR cc_start: 0.8033 (t) cc_final: 0.7669 (t) REVERT: A 386 MET cc_start: 0.6450 (mmp) cc_final: 0.5913 (mmt) REVERT: B 45 MET cc_start: 0.7832 (mtm) cc_final: 0.7151 (ptp) REVERT: B 59 TYR cc_start: 0.4926 (p90) cc_final: 0.4400 (p90) REVERT: B 102 THR cc_start: 0.6938 (t) cc_final: 0.5547 (m) outliers start: 16 outliers final: 9 residues processed: 141 average time/residue: 0.0834 time to fit residues: 15.5065 Evaluate side-chains 143 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 541 ASP Chi-restraints excluded: chain R residue 559 LEU Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 61 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 576 GLN ** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.186049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.159965 restraints weight = 11279.498| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.63 r_work: 0.4026 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8194 Z= 0.146 Angle : 0.593 10.733 11100 Z= 0.323 Chirality : 0.044 0.242 1255 Planarity : 0.004 0.053 1411 Dihedral : 5.088 22.859 1112 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.74 % Allowed : 11.92 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.26), residues: 1008 helix: 1.21 (0.28), residues: 375 sheet: 0.23 (0.34), residues: 203 loop : -1.88 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.017 0.002 TYR B 124 PHE 0.022 0.002 PHE A 212 TRP 0.017 0.002 TRP B 82 HIS 0.007 0.001 HIS R 786 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8192) covalent geometry : angle 0.59315 (11096) SS BOND : bond 0.00239 ( 2) SS BOND : angle 0.21798 ( 4) hydrogen bonds : bond 0.05404 ( 382) hydrogen bonds : angle 4.48340 ( 1047) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: R 745 GLN cc_start: 0.6928 (mp10) cc_final: 0.6691 (mp10) REVERT: R 783 TYR cc_start: 0.6897 (t80) cc_final: 0.6255 (t80) REVERT: A 60 MET cc_start: 0.5204 (OUTLIER) cc_final: 0.4812 (mtm) REVERT: A 350 THR cc_start: 0.7980 (t) cc_final: 0.7640 (t) REVERT: A 386 MET cc_start: 0.6119 (mmp) cc_final: 0.5600 (mmt) REVERT: B 45 MET cc_start: 0.7606 (mtm) cc_final: 0.7259 (ptp) REVERT: B 49 ARG cc_start: 0.7703 (mmm-85) cc_final: 0.7418 (mtp85) REVERT: B 59 TYR cc_start: 0.4624 (p90) cc_final: 0.4162 (p90) REVERT: B 102 THR cc_start: 0.6936 (t) cc_final: 0.5509 (m) outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 0.1125 time to fit residues: 19.7894 Evaluate side-chains 140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 541 ASP Chi-restraints excluded: chain R residue 559 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.183656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.157451 restraints weight = 11189.528| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.59 r_work: 0.4016 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8194 Z= 0.158 Angle : 0.602 10.865 11100 Z= 0.325 Chirality : 0.044 0.222 1255 Planarity : 0.004 0.054 1411 Dihedral : 5.049 23.340 1112 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.66 % Allowed : 12.62 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.26), residues: 1008 helix: 1.25 (0.28), residues: 375 sheet: 0.32 (0.35), residues: 203 loop : -1.87 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 283 TYR 0.018 0.002 TYR B 124 PHE 0.023 0.002 PHE B 199 TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS R 786 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8192) covalent geometry : angle 0.60212 (11096) SS BOND : bond 0.00252 ( 2) SS BOND : angle 0.17385 ( 4) hydrogen bonds : bond 0.05451 ( 382) hydrogen bonds : angle 4.44269 ( 1047) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: R 745 GLN cc_start: 0.6903 (mp10) cc_final: 0.6576 (mp10) REVERT: R 783 TYR cc_start: 0.6887 (t80) cc_final: 0.6317 (t80) REVERT: A 60 MET cc_start: 0.5076 (OUTLIER) cc_final: 0.4803 (ptp) REVERT: A 350 THR cc_start: 0.8000 (t) cc_final: 0.7658 (t) REVERT: A 386 MET cc_start: 0.6096 (mmp) cc_final: 0.5605 (mmt) REVERT: B 45 MET cc_start: 0.7617 (mtm) cc_final: 0.7283 (ptp) REVERT: B 49 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7397 (mtp85) REVERT: B 59 TYR cc_start: 0.4620 (p90) cc_final: 0.4141 (p90) REVERT: B 102 THR cc_start: 0.6981 (t) cc_final: 0.5568 (m) outliers start: 23 outliers final: 14 residues processed: 143 average time/residue: 0.1067 time to fit residues: 20.3124 Evaluate side-chains 144 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 541 ASP Chi-restraints excluded: chain R residue 559 LEU Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.183447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.157298 restraints weight = 11164.368| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.60 r_work: 0.4024 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8194 Z= 0.164 Angle : 0.612 11.723 11100 Z= 0.329 Chirality : 0.044 0.198 1255 Planarity : 0.005 0.055 1411 Dihedral : 4.999 23.629 1112 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.55 % Allowed : 13.31 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.26), residues: 1008 helix: 1.26 (0.28), residues: 375 sheet: 0.32 (0.35), residues: 203 loop : -1.84 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 283 TYR 0.018 0.002 TYR B 124 PHE 0.024 0.002 PHE B 199 TRP 0.016 0.002 TRP B 82 HIS 0.011 0.001 HIS R 786 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8192) covalent geometry : angle 0.61241 (11096) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.17886 ( 4) hydrogen bonds : bond 0.05441 ( 382) hydrogen bonds : angle 4.46533 ( 1047) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: R 783 TYR cc_start: 0.6851 (t80) cc_final: 0.6421 (t80) REVERT: A 60 MET cc_start: 0.5075 (OUTLIER) cc_final: 0.4739 (ptp) REVERT: A 350 THR cc_start: 0.7993 (t) cc_final: 0.7695 (t) REVERT: A 386 MET cc_start: 0.6098 (mmp) cc_final: 0.5593 (mmt) REVERT: B 45 MET cc_start: 0.7631 (mtm) cc_final: 0.7323 (ptp) REVERT: B 49 ARG cc_start: 0.7685 (mmm-85) cc_final: 0.7449 (mtp85) REVERT: B 59 TYR cc_start: 0.4606 (p90) cc_final: 0.4118 (p90) REVERT: B 188 MET cc_start: 0.6983 (mmm) cc_final: 0.6621 (mmt) REVERT: B 297 TRP cc_start: 0.7518 (m100) cc_final: 0.6976 (m100) outliers start: 22 outliers final: 16 residues processed: 132 average time/residue: 0.1021 time to fit residues: 17.8242 Evaluate side-chains 137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 541 ASP Chi-restraints excluded: chain R residue 559 LEU Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 759 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.185644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.159184 restraints weight = 11132.576| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.60 r_work: 0.4020 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8194 Z= 0.169 Angle : 0.621 11.871 11100 Z= 0.333 Chirality : 0.044 0.178 1255 Planarity : 0.005 0.057 1411 Dihedral : 4.998 23.831 1112 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.89 % Allowed : 13.43 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.26), residues: 1008 helix: 1.25 (0.28), residues: 375 sheet: 0.31 (0.35), residues: 202 loop : -1.81 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 283 TYR 0.018 0.002 TYR B 124 PHE 0.025 0.002 PHE B 199 TRP 0.016 0.002 TRP B 169 HIS 0.008 0.001 HIS R 786 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8192) covalent geometry : angle 0.62081 (11096) SS BOND : bond 0.00369 ( 2) SS BOND : angle 0.33334 ( 4) hydrogen bonds : bond 0.05507 ( 382) hydrogen bonds : angle 4.45838 ( 1047) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: R 783 TYR cc_start: 0.6843 (t80) cc_final: 0.6458 (t80) REVERT: A 350 THR cc_start: 0.8009 (t) cc_final: 0.7681 (t) REVERT: A 386 MET cc_start: 0.6085 (mmp) cc_final: 0.5644 (mmt) REVERT: B 45 MET cc_start: 0.7629 (mtm) cc_final: 0.7374 (ptp) REVERT: B 49 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7375 (mtp85) REVERT: B 59 TYR cc_start: 0.4711 (p90) cc_final: 0.4213 (p90) REVERT: B 188 MET cc_start: 0.6949 (mmm) cc_final: 0.6632 (mmt) REVERT: B 234 PHE cc_start: 0.6114 (OUTLIER) cc_final: 0.5104 (m-80) REVERT: B 297 TRP cc_start: 0.7521 (m100) cc_final: 0.6982 (m100) outliers start: 25 outliers final: 18 residues processed: 137 average time/residue: 0.1051 time to fit residues: 19.2196 Evaluate side-chains 140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 541 ASP Chi-restraints excluded: chain R residue 559 LEU Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 759 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 50 optimal weight: 0.0060 chunk 48 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 745 GLN ** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.184671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.158602 restraints weight = 11103.370| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.57 r_work: 0.4035 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8194 Z= 0.147 Angle : 0.609 11.925 11100 Z= 0.326 Chirality : 0.044 0.190 1255 Planarity : 0.005 0.062 1411 Dihedral : 4.881 23.238 1112 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.31 % Allowed : 14.12 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.27), residues: 1008 helix: 1.40 (0.28), residues: 375 sheet: 0.34 (0.35), residues: 202 loop : -1.75 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 283 TYR 0.017 0.002 TYR B 124 PHE 0.021 0.002 PHE B 199 TRP 0.017 0.002 TRP B 82 HIS 0.008 0.001 HIS R 786 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8192) covalent geometry : angle 0.60878 (11096) SS BOND : bond 0.00264 ( 2) SS BOND : angle 0.27600 ( 4) hydrogen bonds : bond 0.05175 ( 382) hydrogen bonds : angle 4.36874 ( 1047) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: R 783 TYR cc_start: 0.6835 (t80) cc_final: 0.6452 (t80) REVERT: A 350 THR cc_start: 0.7864 (t) cc_final: 0.7531 (t) REVERT: A 386 MET cc_start: 0.6080 (mmp) cc_final: 0.5649 (mmt) REVERT: B 45 MET cc_start: 0.7649 (mtm) cc_final: 0.7424 (ptp) REVERT: B 49 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.7396 (mtp85) REVERT: B 59 TYR cc_start: 0.4685 (p90) cc_final: 0.4226 (p90) REVERT: B 102 THR cc_start: 0.6991 (t) cc_final: 0.5539 (m) REVERT: B 188 MET cc_start: 0.6958 (mmm) cc_final: 0.6671 (mmt) REVERT: B 234 PHE cc_start: 0.6063 (OUTLIER) cc_final: 0.4993 (m-80) REVERT: B 297 TRP cc_start: 0.7513 (m100) cc_final: 0.6955 (m100) outliers start: 20 outliers final: 13 residues processed: 134 average time/residue: 0.1086 time to fit residues: 19.3546 Evaluate side-chains 133 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 559 LEU Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.0030 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 88 optimal weight: 0.3980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.187487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.161214 restraints weight = 11052.419| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.60 r_work: 0.4058 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8194 Z= 0.119 Angle : 0.594 12.575 11100 Z= 0.316 Chirality : 0.042 0.170 1255 Planarity : 0.004 0.065 1411 Dihedral : 4.700 24.605 1112 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.50 % Allowed : 14.70 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.27), residues: 1008 helix: 1.57 (0.28), residues: 375 sheet: 0.37 (0.36), residues: 205 loop : -1.69 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 283 TYR 0.016 0.001 TYR B 124 PHE 0.015 0.001 PHE A 212 TRP 0.021 0.002 TRP B 82 HIS 0.007 0.001 HIS R 786 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8192) covalent geometry : angle 0.59441 (11096) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.37212 ( 4) hydrogen bonds : bond 0.04568 ( 382) hydrogen bonds : angle 4.23571 ( 1047) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 783 TYR cc_start: 0.6820 (t80) cc_final: 0.6440 (t80) REVERT: A 386 MET cc_start: 0.6038 (mmp) cc_final: 0.5621 (mmt) REVERT: B 49 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.7356 (mtp85) REVERT: B 59 TYR cc_start: 0.4610 (p90) cc_final: 0.4172 (p90) REVERT: B 101 MET cc_start: 0.6082 (mtt) cc_final: 0.5251 (mtt) REVERT: B 102 THR cc_start: 0.7026 (t) cc_final: 0.5601 (m) REVERT: B 188 MET cc_start: 0.7093 (mmm) cc_final: 0.6804 (mmt) REVERT: B 234 PHE cc_start: 0.6036 (OUTLIER) cc_final: 0.4970 (m-80) REVERT: B 297 TRP cc_start: 0.7490 (m100) cc_final: 0.6893 (m100) outliers start: 13 outliers final: 12 residues processed: 134 average time/residue: 0.1064 time to fit residues: 19.1448 Evaluate side-chains 138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 559 LEU Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 576 GLN ** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.183851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.157559 restraints weight = 11132.348| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.59 r_work: 0.4012 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 8194 Z= 0.194 Angle : 0.665 10.973 11100 Z= 0.356 Chirality : 0.045 0.167 1255 Planarity : 0.005 0.078 1411 Dihedral : 5.035 23.739 1112 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.20 % Allowed : 14.70 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.26), residues: 1008 helix: 1.34 (0.27), residues: 378 sheet: 0.20 (0.35), residues: 208 loop : -1.79 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 283 TYR 0.019 0.002 TYR D 95 PHE 0.025 0.002 PHE B 199 TRP 0.022 0.002 TRP B 82 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 8192) covalent geometry : angle 0.66457 (11096) SS BOND : bond 0.00441 ( 2) SS BOND : angle 0.47146 ( 4) hydrogen bonds : bond 0.05661 ( 382) hydrogen bonds : angle 4.51742 ( 1047) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: R 745 GLN cc_start: 0.6923 (mp-120) cc_final: 0.6547 (mp10) REVERT: R 783 TYR cc_start: 0.6906 (t80) cc_final: 0.6484 (t80) REVERT: A 342 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6674 (ttp-170) REVERT: A 386 MET cc_start: 0.6088 (mmp) cc_final: 0.5631 (mmt) REVERT: B 49 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.7430 (mtp85) REVERT: B 59 TYR cc_start: 0.4629 (p90) cc_final: 0.4171 (p90) REVERT: B 82 TRP cc_start: 0.6708 (m100) cc_final: 0.6394 (m100) REVERT: B 188 MET cc_start: 0.6954 (mmm) cc_final: 0.6674 (mmt) REVERT: B 234 PHE cc_start: 0.6259 (OUTLIER) cc_final: 0.5149 (m-80) REVERT: B 297 TRP cc_start: 0.7529 (m100) cc_final: 0.6986 (m100) outliers start: 19 outliers final: 16 residues processed: 134 average time/residue: 0.1117 time to fit residues: 19.7309 Evaluate side-chains 138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 559 LEU Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.184248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.158061 restraints weight = 11078.649| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.57 r_work: 0.4021 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 8194 Z= 0.182 Angle : 0.661 10.764 11100 Z= 0.353 Chirality : 0.045 0.203 1255 Planarity : 0.005 0.074 1411 Dihedral : 5.044 27.001 1112 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.08 % Allowed : 15.05 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.26), residues: 1008 helix: 1.23 (0.27), residues: 384 sheet: 0.11 (0.34), residues: 208 loop : -1.84 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 283 TYR 0.018 0.002 TYR B 124 PHE 0.025 0.002 PHE B 199 TRP 0.023 0.002 TRP B 82 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8192) covalent geometry : angle 0.66125 (11096) SS BOND : bond 0.00432 ( 2) SS BOND : angle 0.42064 ( 4) hydrogen bonds : bond 0.05590 ( 382) hydrogen bonds : angle 4.51092 ( 1047) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2790.98 seconds wall clock time: 48 minutes 22.95 seconds (2902.95 seconds total)