Starting phenix.real_space_refine on Tue Sep 24 12:11:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydp_33755/09_2024/7ydp_33755.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydp_33755/09_2024/7ydp_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydp_33755/09_2024/7ydp_33755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydp_33755/09_2024/7ydp_33755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydp_33755/09_2024/7ydp_33755.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydp_33755/09_2024/7ydp_33755.cif" } resolution = 3.1 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= 0.020 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, '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: 5.25, per 1000 atoms: 0.65 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: 2.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.93 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: 2.21 Time building geometry restraints manager: 2.43 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: 0.890 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 21.860 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- 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 8192 Z= 0.315 Angle : 0.733 7.803 11096 Z= 0.431 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 (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: -1.21 (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 TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS R 583 PHE 0.030 0.003 PHE B 151 TYR 0.022 0.002 TYR B 124 ARG 0.007 0.000 ARG B 48 *********************** 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 fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.834 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: 0.3897 (p90) REVERT: B 102 THR cc_start: 0.6778 (t) cc_final: 0.5467 (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: 0.6784 (m100) REVERT: B 304 ARG cc_start: 0.6952 (ttp-170) cc_final: 0.6455 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2119 time to fit residues: 41.0480 Evaluate side-chains 136 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 41 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8192 Z= 0.200 Angle : 0.623 10.700 11096 Z= 0.337 Chirality : 0.043 0.149 1255 Planarity : 0.005 0.055 1411 Dihedral : 5.319 23.108 1112 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.93 % Allowed : 7.29 % Favored : 91.78 % 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: -0.66 (0.26), residues: 1008 helix: 0.99 (0.28), residues: 372 sheet: 0.06 (0.33), residues: 208 loop : -2.03 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 297 HIS 0.006 0.001 HIS R 583 PHE 0.019 0.002 PHE A 212 TYR 0.018 0.002 TYR B 124 ARG 0.004 0.000 ARG B 49 *********************** 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 139 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 576 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: R 783 TYR cc_start: 0.6745 (t80) cc_final: 0.5910 (t80) REVERT: A 350 THR cc_start: 0.8094 (t) cc_final: 0.7738 (t) REVERT: A 386 MET cc_start: 0.5076 (mmp) cc_final: 0.4695 (mmt) REVERT: B 59 TYR cc_start: 0.4430 (p90) cc_final: 0.3996 (p90) REVERT: B 102 THR cc_start: 0.6765 (t) cc_final: 0.5527 (m) REVERT: B 217 MET cc_start: 0.6334 (tmm) cc_final: 0.6121 (tmm) REVERT: B 297 TRP cc_start: 0.7183 (m100) cc_final: 0.6295 (m100) outliers start: 8 outliers final: 4 residues processed: 136 average time/residue: 0.2171 time to fit residues: 39.8222 Evaluate side-chains 131 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 273 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8192 Z= 0.230 Angle : 0.599 10.306 11096 Z= 0.328 Chirality : 0.043 0.147 1255 Planarity : 0.004 0.053 1411 Dihedral : 5.150 22.243 1112 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.27 % Allowed : 9.49 % Favored : 89.24 % 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: -0.49 (0.26), residues: 1008 helix: 1.16 (0.28), residues: 373 sheet: 0.08 (0.33), residues: 210 loop : -1.95 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.008 0.001 HIS R 786 PHE 0.022 0.002 PHE A 212 TYR 0.017 0.002 TYR B 124 ARG 0.005 0.000 ARG B 49 *********************** 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 139 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: R 576 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7292 (mp-120) REVERT: R 745 GLN cc_start: 0.6868 (mp10) cc_final: 0.6530 (mp10) REVERT: R 783 TYR cc_start: 0.6790 (t80) cc_final: 0.6085 (t80) REVERT: A 60 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4783 (mtm) REVERT: A 221 MET cc_start: 0.6563 (mtt) cc_final: 0.6312 (mtp) REVERT: A 350 THR cc_start: 0.8080 (t) cc_final: 0.7753 (t) REVERT: A 386 MET cc_start: 0.5070 (mmp) cc_final: 0.4654 (mmt) REVERT: B 45 MET cc_start: 0.7264 (mtm) cc_final: 0.6840 (ptp) REVERT: B 49 ARG cc_start: 0.7389 (mmm-85) cc_final: 0.7062 (mtp85) REVERT: B 59 TYR cc_start: 0.4334 (p90) cc_final: 0.3862 (p90) REVERT: B 102 THR cc_start: 0.6833 (t) cc_final: 0.5511 (m) REVERT: B 262 MET cc_start: 0.5969 (tmm) cc_final: 0.5688 (tmm) outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 0.2258 time to fit residues: 39.4231 Evaluate side-chains 135 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 A residue 378 ASP Chi-restraints excluded: chain D residue 48 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8192 Z= 0.251 Angle : 0.600 9.838 11096 Z= 0.327 Chirality : 0.044 0.265 1255 Planarity : 0.004 0.054 1411 Dihedral : 5.116 23.401 1112 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.08 % Allowed : 11.81 % Favored : 86.11 % 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: -0.39 (0.26), residues: 1008 helix: 1.19 (0.28), residues: 375 sheet: 0.19 (0.34), residues: 209 loop : -1.89 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS R 786 PHE 0.025 0.002 PHE A 212 TYR 0.018 0.002 TYR B 124 ARG 0.006 0.000 ARG B 314 *********************** 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 144 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: R 745 GLN cc_start: 0.6842 (mp10) cc_final: 0.6604 (mp10) REVERT: R 783 TYR cc_start: 0.6768 (t80) cc_final: 0.6222 (t80) REVERT: A 60 MET cc_start: 0.4994 (OUTLIER) cc_final: 0.4613 (mtm) REVERT: A 350 THR cc_start: 0.8072 (t) cc_final: 0.7803 (t) REVERT: A 386 MET cc_start: 0.5056 (mmp) cc_final: 0.4649 (mmt) REVERT: B 45 MET cc_start: 0.7262 (mtm) cc_final: 0.6925 (ptp) REVERT: B 48 ARG cc_start: 0.7057 (mmt-90) cc_final: 0.6701 (mpt180) REVERT: B 49 ARG cc_start: 0.7373 (mmm-85) cc_final: 0.7128 (mtp85) REVERT: B 59 TYR cc_start: 0.4410 (p90) cc_final: 0.4018 (p90) REVERT: B 102 THR cc_start: 0.6907 (t) cc_final: 0.5490 (m) outliers start: 18 outliers final: 10 residues processed: 136 average time/residue: 0.2273 time to fit residues: 40.8322 Evaluate side-chains 136 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 79 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 8192 Z= 0.371 Angle : 0.670 10.853 11096 Z= 0.363 Chirality : 0.047 0.223 1255 Planarity : 0.005 0.060 1411 Dihedral : 5.397 24.710 1112 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.66 % Allowed : 12.73 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1008 helix: 1.02 (0.28), residues: 375 sheet: 0.06 (0.33), residues: 213 loop : -2.00 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.007 0.002 HIS R 786 PHE 0.035 0.003 PHE B 199 TYR 0.022 0.002 TYR B 124 ARG 0.007 0.000 ARG B 314 *********************** 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 155 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: R 745 GLN cc_start: 0.6848 (mp10) cc_final: 0.6600 (mp10) REVERT: R 783 TYR cc_start: 0.6802 (t80) cc_final: 0.6403 (t80) REVERT: A 60 MET cc_start: 0.5021 (OUTLIER) cc_final: 0.4655 (ptp) REVERT: A 386 MET cc_start: 0.5050 (mmp) cc_final: 0.4681 (mmt) REVERT: B 45 MET cc_start: 0.7263 (mtm) cc_final: 0.6958 (ptp) REVERT: B 48 ARG cc_start: 0.7077 (mmt-90) cc_final: 0.6675 (mpt180) REVERT: B 49 ARG cc_start: 0.7433 (mmm-85) cc_final: 0.7230 (mtp85) REVERT: B 59 TYR cc_start: 0.4388 (p90) cc_final: 0.4042 (p90) outliers start: 23 outliers final: 17 residues processed: 145 average time/residue: 0.2240 time to fit residues: 43.1979 Evaluate side-chains 147 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8192 Z= 0.258 Angle : 0.627 11.153 11096 Z= 0.340 Chirality : 0.044 0.200 1255 Planarity : 0.005 0.052 1411 Dihedral : 5.172 23.760 1112 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.55 % Allowed : 13.66 % 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 (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: -0.42 (0.26), residues: 1008 helix: 1.13 (0.28), residues: 376 sheet: 0.13 (0.34), residues: 214 loop : -1.87 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.007 0.001 HIS R 786 PHE 0.023 0.002 PHE B 199 TYR 0.018 0.002 TYR B 124 ARG 0.004 0.000 ARG B 314 *********************** 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 148 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: R 745 GLN cc_start: 0.6772 (mp10) cc_final: 0.6423 (mp10) REVERT: R 783 TYR cc_start: 0.6677 (t80) cc_final: 0.6381 (t80) REVERT: A 60 MET cc_start: 0.4920 (OUTLIER) cc_final: 0.4609 (ptp) REVERT: A 350 THR cc_start: 0.8034 (t) cc_final: 0.7721 (t) REVERT: A 386 MET cc_start: 0.5047 (mmp) cc_final: 0.4694 (mmt) REVERT: B 45 MET cc_start: 0.7262 (mtm) cc_final: 0.6988 (ptp) REVERT: B 49 ARG cc_start: 0.7353 (mmm-85) cc_final: 0.7062 (mtp85) REVERT: B 59 TYR cc_start: 0.4252 (p90) cc_final: 0.3925 (p90) REVERT: B 297 TRP cc_start: 0.7286 (m100) cc_final: 0.6799 (m100) outliers start: 22 outliers final: 14 residues processed: 139 average time/residue: 0.2360 time to fit residues: 43.2499 Evaluate side-chains 138 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 285 LEU Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 0.0670 chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 58 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.2656 ------------------------------------------------------------------------------- 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** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8192 Z= 0.156 Angle : 0.576 12.266 11096 Z= 0.307 Chirality : 0.042 0.193 1255 Planarity : 0.004 0.054 1411 Dihedral : 4.714 21.687 1112 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.85 % Allowed : 14.81 % 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: -0.13 (0.27), residues: 1008 helix: 1.41 (0.28), residues: 375 sheet: 0.32 (0.35), residues: 211 loop : -1.73 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.009 0.001 HIS R 786 PHE 0.012 0.001 PHE B 199 TYR 0.017 0.001 TYR B 124 ARG 0.003 0.000 ARG B 314 *********************** 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 151 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: R 783 TYR cc_start: 0.6640 (t80) cc_final: 0.6397 (t80) REVERT: A 309 GLU cc_start: 0.6490 (tp30) cc_final: 0.6270 (tp30) REVERT: A 350 THR cc_start: 0.7842 (t) cc_final: 0.7523 (t) REVERT: A 386 MET cc_start: 0.5024 (mmp) cc_final: 0.4793 (mmt) REVERT: B 59 TYR cc_start: 0.4223 (p90) cc_final: 0.3885 (p90) REVERT: B 101 MET cc_start: 0.5893 (mtt) cc_final: 0.5270 (mtt) REVERT: B 102 THR cc_start: 0.6846 (t) cc_final: 0.5561 (m) REVERT: B 234 PHE cc_start: 0.5918 (OUTLIER) cc_final: 0.4906 (m-80) REVERT: B 297 TRP cc_start: 0.7232 (m100) cc_final: 0.6654 (m100) outliers start: 16 outliers final: 9 residues processed: 141 average time/residue: 0.2265 time to fit residues: 42.4005 Evaluate side-chains 146 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 0.0040 chunk 86 optimal weight: 0.0970 chunk 91 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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 A 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8192 Z= 0.185 Angle : 0.589 11.586 11096 Z= 0.314 Chirality : 0.043 0.178 1255 Planarity : 0.004 0.053 1411 Dihedral : 4.708 22.471 1112 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.50 % Allowed : 15.51 % Favored : 82.99 % 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: 0.01 (0.27), residues: 1008 helix: 1.46 (0.28), residues: 376 sheet: 0.58 (0.36), residues: 202 loop : -1.66 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.008 0.001 HIS R 786 PHE 0.016 0.001 PHE B 199 TYR 0.015 0.001 TYR B 124 ARG 0.007 0.000 ARG A 283 *********************** 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 140 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: R 783 TYR cc_start: 0.6634 (t80) cc_final: 0.6413 (t80) REVERT: A 386 MET cc_start: 0.5016 (mmp) cc_final: 0.4790 (mmt) REVERT: B 59 TYR cc_start: 0.4267 (p90) cc_final: 0.3938 (p90) REVERT: B 102 THR cc_start: 0.6904 (t) cc_final: 0.5535 (m) REVERT: B 234 PHE cc_start: 0.5959 (OUTLIER) cc_final: 0.4926 (m-80) REVERT: B 297 TRP cc_start: 0.7258 (m100) cc_final: 0.6681 (m100) outliers start: 13 outliers final: 10 residues processed: 133 average time/residue: 0.2343 time to fit residues: 41.2091 Evaluate side-chains 137 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8192 Z= 0.257 Angle : 0.630 12.635 11096 Z= 0.338 Chirality : 0.044 0.159 1255 Planarity : 0.005 0.062 1411 Dihedral : 4.886 24.489 1112 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.97 % Allowed : 15.74 % Favored : 82.29 % 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: -0.12 (0.27), residues: 1008 helix: 1.39 (0.28), residues: 375 sheet: 0.46 (0.35), residues: 202 loop : -1.73 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.024 0.002 PHE B 199 TYR 0.018 0.002 TYR B 124 ARG 0.015 0.000 ARG A 283 *********************** 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 fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: R 783 TYR cc_start: 0.6671 (t80) cc_final: 0.6450 (t80) REVERT: A 386 MET cc_start: 0.5026 (mmp) cc_final: 0.4796 (mmt) REVERT: B 59 TYR cc_start: 0.4271 (p90) cc_final: 0.3901 (p90) REVERT: B 297 TRP cc_start: 0.7278 (m100) cc_final: 0.6719 (m100) REVERT: B 304 ARG cc_start: 0.6958 (ttm110) cc_final: 0.6747 (ttp-170) outliers start: 17 outliers final: 16 residues processed: 133 average time/residue: 0.2323 time to fit residues: 40.8756 Evaluate side-chains 138 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 369 THR 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 93 ILE 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 285 LEU Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8192 Z= 0.258 Angle : 0.636 10.366 11096 Z= 0.341 Chirality : 0.044 0.182 1255 Planarity : 0.005 0.071 1411 Dihedral : 4.943 26.929 1112 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.08 % Allowed : 15.62 % Favored : 82.29 % 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: -0.17 (0.27), residues: 1008 helix: 1.31 (0.27), residues: 378 sheet: 0.40 (0.35), residues: 202 loop : -1.73 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.006 0.001 HIS A 220 PHE 0.024 0.002 PHE A 212 TYR 0.018 0.002 TYR B 124 ARG 0.017 0.000 ARG A 283 ********************** 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 142 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 783 TYR cc_start: 0.6704 (t80) cc_final: 0.6437 (t80) REVERT: A 386 MET cc_start: 0.5031 (mmp) cc_final: 0.4802 (mmt) REVERT: B 59 TYR cc_start: 0.4277 (p90) cc_final: 0.3939 (p90) REVERT: B 102 THR cc_start: 0.6979 (t) cc_final: 0.5603 (m) REVERT: B 234 PHE cc_start: 0.5951 (OUTLIER) cc_final: 0.4934 (m-80) REVERT: B 297 TRP cc_start: 0.7275 (m100) cc_final: 0.6722 (m100) REVERT: B 304 ARG cc_start: 0.6972 (ttm110) cc_final: 0.6753 (ttp-170) outliers start: 18 outliers final: 16 residues processed: 134 average time/residue: 0.2297 time to fit residues: 40.6942 Evaluate side-chains 141 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.183629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.157479 restraints weight = 11065.053| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.58 r_work: 0.4015 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 8192 Z= 0.276 Angle : 0.654 10.749 11096 Z= 0.351 Chirality : 0.045 0.148 1255 Planarity : 0.005 0.073 1411 Dihedral : 4.983 23.801 1112 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.31 % Allowed : 15.74 % Favored : 81.94 % 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: -0.20 (0.26), residues: 1008 helix: 1.29 (0.27), residues: 378 sheet: 0.44 (0.36), residues: 199 loop : -1.77 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS R 786 PHE 0.025 0.002 PHE B 199 TYR 0.018 0.002 TYR B 124 ARG 0.018 0.000 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.27 seconds wall clock time: 39 minutes 58.00 seconds (2398.00 seconds total)