Starting phenix.real_space_refine on Fri Aug 22 21:12:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nox_49620/08_2025/9nox_49620.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nox_49620/08_2025/9nox_49620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nox_49620/08_2025/9nox_49620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nox_49620/08_2025/9nox_49620.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nox_49620/08_2025/9nox_49620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nox_49620/08_2025/9nox_49620.map" } resolution = 3.0 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= 0.000 sd= 0.027 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 58 5.16 5 C 5052 2.51 5 N 1369 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7965 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1954 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 400 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2031 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 1 Time building chain proxies: 1.54, per 1000 atoms: 0.19 Number of scatterers: 7965 At special positions: 0 Unit cell: (85.592, 97.937, 125.096, 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 58 16.00 O 1486 8.00 N 1369 7.00 C 5052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 296.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 44.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 7 through 35 removed outlier: 3.610A pdb=" N VAL B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 61 removed outlier: 3.695A pdb=" N ILE B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 removed outlier: 3.606A pdb=" N GLN B 102 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 105 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP B 106 " --> pdb=" O CYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 149 through 160 Processing helix chain 'B' and resid 163 through 168 removed outlier: 4.276A pdb=" N TYR B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 172 removed outlier: 3.711A pdb=" N ALA B 172 " --> pdb=" O PRO B 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 172' Processing helix chain 'B' and resid 187 through 209 removed outlier: 4.124A pdb=" N ILE B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 247 Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.594A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.739A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.663A pdb=" N ASN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'A' and resid 563 through 590 Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 601 through 617 removed outlier: 3.538A pdb=" N PHE A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.644A pdb=" N TYR A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 622 " --> pdb=" O VAL A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 622' Processing helix chain 'A' and resid 626 through 636 removed outlier: 4.018A pdb=" N GLN A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 660 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 676 through 699 removed outlier: 3.782A pdb=" N MET A 682 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 683 " --> pdb=" O TYR A 679 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.774A pdb=" N PHE A 730 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 750 No H-bonds generated for 'chain 'A' and resid 748 through 750' Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.095A pdb=" N SER A 781 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 818 removed outlier: 4.670A pdb=" N TYR A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Proline residue: A 810 - end of helix Processing helix chain 'A' and resid 819 through 822 Processing helix chain 'A' and resid 823 through 836 Processing sheet with id=AA1, first strand: chain 'B' and resid 76 through 79 removed outlier: 8.952A pdb=" N ALA B 109 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG B 39 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE B 111 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 41 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL B 113 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 43 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP B 115 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE B 110 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE B 146 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE B 112 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN B 148 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 114 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL B 143 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N HIS B 218 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 145 " --> pdb=" O HIS B 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.176A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.852A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C 88 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.177A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.439A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.559A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.664A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.076A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.820A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1191 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: 1.15 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2599 1.35 - 1.46: 1940 1.46 - 1.58: 3506 1.58 - 1.70: 0 1.70 - 1.81: 84 Bond restraints: 8129 Sorted by residual: bond pdb=" N ASP B 179 " pdb=" CA ASP B 179 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.67e+00 bond pdb=" C ASP B 179 " pdb=" O ASP B 179 " ideal model delta sigma weight residual 1.235 1.250 -0.015 1.26e-02 6.30e+03 1.41e+00 bond pdb=" CG ARG B 203 " pdb=" CD ARG B 203 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.65e-01 bond pdb=" CA THR C 196 " pdb=" CB THR C 196 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 7.16e-01 bond pdb=" N PRO A 624 " pdb=" CA PRO A 624 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 7.04e-01 ... (remaining 8124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 10866 1.84 - 3.69: 124 3.69 - 5.53: 14 5.53 - 7.37: 4 7.37 - 9.22: 3 Bond angle restraints: 11011 Sorted by residual: angle pdb=" CB MET C 325 " pdb=" CG MET C 325 " pdb=" SD MET C 325 " ideal model delta sigma weight residual 112.70 121.92 -9.22 3.00e+00 1.11e-01 9.44e+00 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 125.20 -8.90 3.50e+00 8.16e-02 6.46e+00 angle pdb=" CA ASP B 179 " pdb=" CB ASP B 179 " pdb=" CG ASP B 179 " ideal model delta sigma weight residual 112.60 114.89 -2.29 1.00e+00 1.00e+00 5.24e+00 angle pdb=" CA GLY B 91 " pdb=" C GLY B 91 " pdb=" N GLY B 92 " ideal model delta sigma weight residual 114.61 117.41 -2.80 1.26e+00 6.30e-01 4.95e+00 angle pdb=" CA LEU A 798 " pdb=" CB LEU A 798 " pdb=" CG LEU A 798 " ideal model delta sigma weight residual 116.30 123.99 -7.69 3.50e+00 8.16e-02 4.82e+00 ... (remaining 11006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4075 17.03 - 34.06: 535 34.06 - 51.08: 199 51.08 - 68.11: 31 68.11 - 85.14: 8 Dihedral angle restraints: 4848 sinusoidal: 1899 harmonic: 2949 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -133.00 47.00 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CA ASP C 76 " pdb=" CB ASP C 76 " pdb=" CG ASP C 76 " pdb=" OD1 ASP C 76 " ideal model delta sinusoidal sigma weight residual -30.00 -89.62 59.62 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CG ARG B 94 " pdb=" CD ARG B 94 " pdb=" NE ARG B 94 " pdb=" CZ ARG B 94 " ideal model delta sinusoidal sigma weight residual 90.00 134.96 -44.96 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 915 0.042 - 0.083: 237 0.083 - 0.125: 82 0.125 - 0.166: 5 0.166 - 0.208: 1 Chirality restraints: 1240 Sorted by residual: chirality pdb=" CB VAL A 797 " pdb=" CA VAL A 797 " pdb=" CG1 VAL A 797 " pdb=" CG2 VAL A 797 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE A 695 " pdb=" CA ILE A 695 " pdb=" CG1 ILE A 695 " pdb=" CG2 ILE A 695 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1237 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 196 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C THR C 196 " -0.028 2.00e-02 2.50e+03 pdb=" O THR C 196 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG C 197 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 809 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 810 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 810 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 810 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 564 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 565 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " -0.021 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 3355 2.92 - 3.42: 7767 3.42 - 3.91: 13391 3.91 - 4.41: 15121 4.41 - 4.90: 25891 Nonbonded interactions: 65525 Sorted by model distance: nonbonded pdb=" NE2 HIS C 225 " pdb=" OG1 THR C 243 " model vdw 2.428 3.120 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.554 3.040 nonbonded pdb=" N ASP C 38 " pdb=" OD1 ASP C 38 " model vdw 2.604 3.120 nonbonded pdb=" O LEU B 202 " pdb=" OG SER B 205 " model vdw 2.606 3.040 nonbonded pdb=" C SER B 117 " pdb=" OG SER B 117 " model vdw 2.625 2.616 ... (remaining 65520 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: 9.520 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.280 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.003 0.036 8131 Z= 0.122 Angle : 0.522 9.216 11015 Z= 0.272 Chirality : 0.041 0.208 1240 Planarity : 0.004 0.039 1407 Dihedral : 17.591 85.140 2940 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.08 % Allowed : 28.84 % Favored : 69.09 % 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: 0.99 (0.27), residues: 1001 helix: 2.35 (0.26), residues: 389 sheet: -0.60 (0.35), residues: 216 loop : -0.24 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 19 TYR 0.013 0.001 TYR A 621 PHE 0.023 0.001 PHE A 761 TRP 0.009 0.001 TRP B 100 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8129) covalent geometry : angle 0.52187 (11011) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.54888 ( 4) hydrogen bonds : bond 0.16061 ( 416) hydrogen bonds : angle 6.11838 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7671 (m-30) cc_final: 0.7047 (m-30) REVERT: B 55 LYS cc_start: 0.7000 (mptt) cc_final: 0.6083 (mtpt) REVERT: B 74 PHE cc_start: 0.7630 (t80) cc_final: 0.6973 (m-80) REVERT: B 124 GLU cc_start: 0.8035 (tt0) cc_final: 0.7446 (tp30) REVERT: B 148 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8762 (m110) REVERT: B 167 TYR cc_start: 0.8173 (m-80) cc_final: 0.7727 (m-80) REVERT: B 170 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7965 (pt0) REVERT: C 19 ARG cc_start: 0.7853 (mtp-110) cc_final: 0.7462 (ttm110) REVERT: C 76 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8491 (p0) REVERT: C 175 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7904 (mm-40) REVERT: C 197 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7593 (mtm-85) REVERT: C 214 ARG cc_start: 0.8021 (mmt-90) cc_final: 0.7782 (mmm160) REVERT: C 215 GLU cc_start: 0.8249 (mp0) cc_final: 0.7683 (mp0) REVERT: D 20 LYS cc_start: 0.7977 (mmmt) cc_final: 0.7622 (mtpm) REVERT: D 46 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8104 (mptp) REVERT: A 621 TYR cc_start: 0.4495 (OUTLIER) cc_final: 0.3351 (m-80) REVERT: A 685 ILE cc_start: 0.7618 (mm) cc_final: 0.7298 (tp) REVERT: A 724 TYR cc_start: 0.3863 (m-80) cc_final: 0.3660 (m-80) REVERT: A 780 MET cc_start: 0.4310 (mmm) cc_final: 0.2492 (tpp) outliers start: 18 outliers final: 11 residues processed: 130 average time/residue: 0.4638 time to fit residues: 64.4220 Evaluate side-chains 129 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 836 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.0070 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.163892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119852 restraints weight = 9585.807| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.26 r_work: 0.3311 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8131 Z= 0.152 Angle : 0.526 7.353 11015 Z= 0.275 Chirality : 0.042 0.141 1240 Planarity : 0.004 0.040 1407 Dihedral : 6.361 58.628 1136 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.58 % Allowed : 26.76 % Favored : 69.67 % 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: 1.07 (0.26), residues: 1001 helix: 2.40 (0.26), residues: 390 sheet: -0.39 (0.35), residues: 214 loop : -0.32 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.011 0.001 TYR A 621 PHE 0.012 0.001 PHE A 761 TRP 0.011 0.001 TRP B 100 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8129) covalent geometry : angle 0.52585 (11011) SS BOND : bond 0.00287 ( 2) SS BOND : angle 1.22197 ( 4) hydrogen bonds : bond 0.04281 ( 416) hydrogen bonds : angle 4.59234 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7743 (m-30) cc_final: 0.7086 (m-30) REVERT: B 55 LYS cc_start: 0.7008 (mptt) cc_final: 0.6138 (mtpt) REVERT: B 74 PHE cc_start: 0.7717 (t80) cc_final: 0.7054 (m-80) REVERT: B 95 ASP cc_start: 0.7485 (p0) cc_final: 0.7280 (p0) REVERT: B 124 GLU cc_start: 0.8161 (tt0) cc_final: 0.7543 (tp30) REVERT: B 167 TYR cc_start: 0.8188 (m-80) cc_final: 0.7726 (m-80) REVERT: B 170 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7974 (pt0) REVERT: C 65 THR cc_start: 0.8373 (m) cc_final: 0.8119 (p) REVERT: C 197 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.7583 (mtm-85) REVERT: C 214 ARG cc_start: 0.8028 (mmt-90) cc_final: 0.7764 (mmm160) REVERT: C 215 GLU cc_start: 0.8251 (mp0) cc_final: 0.7667 (mp0) REVERT: C 217 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7870 (ppp) REVERT: D 20 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7734 (mtpm) REVERT: D 46 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8246 (mptt) REVERT: E 76 LYS cc_start: 0.8181 (ptpp) cc_final: 0.7596 (pttt) REVERT: A 621 TYR cc_start: 0.4310 (OUTLIER) cc_final: 0.3202 (m-80) REVERT: A 780 MET cc_start: 0.4425 (mmm) cc_final: 0.2577 (tpp) outliers start: 31 outliers final: 12 residues processed: 144 average time/residue: 0.4313 time to fit residues: 66.6677 Evaluate side-chains 132 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 765 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 4 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 42 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 62 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN C 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.166710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123896 restraints weight = 9484.117| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.12 r_work: 0.3380 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8131 Z= 0.100 Angle : 0.480 8.177 11015 Z= 0.249 Chirality : 0.041 0.150 1240 Planarity : 0.003 0.039 1407 Dihedral : 5.019 53.635 1118 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.84 % Allowed : 25.61 % Favored : 69.55 % 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: 1.28 (0.27), residues: 1001 helix: 2.71 (0.26), residues: 385 sheet: -0.24 (0.36), residues: 202 loop : -0.35 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.011 0.001 TYR E 80 PHE 0.024 0.001 PHE A 684 TRP 0.012 0.001 TRP B 100 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 8129) covalent geometry : angle 0.48013 (11011) SS BOND : bond 0.00409 ( 2) SS BOND : angle 0.97209 ( 4) hydrogen bonds : bond 0.03416 ( 416) hydrogen bonds : angle 4.21296 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.307 Fit side-chains REVERT: B 30 ASP cc_start: 0.7652 (m-30) cc_final: 0.7002 (m-30) REVERT: B 55 LYS cc_start: 0.7043 (mptt) cc_final: 0.6132 (mtpt) REVERT: B 74 PHE cc_start: 0.7705 (t80) cc_final: 0.7055 (m-80) REVERT: B 95 ASP cc_start: 0.7405 (p0) cc_final: 0.7200 (p0) REVERT: B 124 GLU cc_start: 0.8120 (tt0) cc_final: 0.7456 (tp30) REVERT: B 148 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8414 (m110) REVERT: B 161 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7804 (mttt) REVERT: B 167 TYR cc_start: 0.8181 (m-80) cc_final: 0.7755 (m-80) REVERT: B 170 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7984 (pt0) REVERT: C 197 ARG cc_start: 0.8247 (mtp-110) cc_final: 0.7560 (mtm-85) REVERT: C 214 ARG cc_start: 0.7995 (mmt-90) cc_final: 0.7747 (mmm160) REVERT: C 215 GLU cc_start: 0.8268 (mp0) cc_final: 0.7680 (mp0) REVERT: C 217 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7847 (ppp) REVERT: D 20 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7714 (mtpm) REVERT: D 46 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8213 (mptt) REVERT: E 76 LYS cc_start: 0.8066 (ptpp) cc_final: 0.7447 (pttt) REVERT: A 613 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7446 (t) REVERT: A 621 TYR cc_start: 0.4166 (OUTLIER) cc_final: 0.3017 (m-80) REVERT: A 780 MET cc_start: 0.4483 (mmm) cc_final: 0.2559 (tpp) REVERT: A 803 ILE cc_start: 0.7846 (mt) cc_final: 0.7546 (tp) outliers start: 42 outliers final: 16 residues processed: 160 average time/residue: 0.4825 time to fit residues: 82.7285 Evaluate side-chains 142 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 836 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN E 77 ASN A 755 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118898 restraints weight = 9759.154| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.24 r_work: 0.3294 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8131 Z= 0.182 Angle : 0.533 7.447 11015 Z= 0.276 Chirality : 0.043 0.158 1240 Planarity : 0.004 0.040 1407 Dihedral : 5.100 50.933 1117 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.96 % Allowed : 26.18 % Favored : 68.86 % 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: 1.12 (0.26), residues: 1001 helix: 2.59 (0.26), residues: 385 sheet: -0.51 (0.35), residues: 210 loop : -0.32 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 651 TYR 0.012 0.001 TYR A 621 PHE 0.012 0.001 PHE C 151 TRP 0.011 0.002 TRP E 47 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8129) covalent geometry : angle 0.53218 (11011) SS BOND : bond 0.00312 ( 2) SS BOND : angle 1.35563 ( 4) hydrogen bonds : bond 0.03659 ( 416) hydrogen bonds : angle 4.22615 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7700 (m-30) cc_final: 0.7010 (m-30) REVERT: B 55 LYS cc_start: 0.6986 (mptt) cc_final: 0.6090 (mtpt) REVERT: B 74 PHE cc_start: 0.7765 (t80) cc_final: 0.7102 (m-80) REVERT: B 95 ASP cc_start: 0.7493 (p0) cc_final: 0.7253 (p0) REVERT: B 118 ASP cc_start: 0.7841 (t0) cc_final: 0.7425 (t0) REVERT: B 124 GLU cc_start: 0.8156 (tt0) cc_final: 0.7451 (tp30) REVERT: B 148 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8668 (m110) REVERT: B 161 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7749 (mttt) REVERT: B 167 TYR cc_start: 0.8173 (m-80) cc_final: 0.7701 (m-80) REVERT: B 170 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7995 (pt0) REVERT: C 65 THR cc_start: 0.8453 (m) cc_final: 0.8191 (p) REVERT: C 76 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8441 (p0) REVERT: C 197 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.7550 (mtm-85) REVERT: C 214 ARG cc_start: 0.8051 (mmt-90) cc_final: 0.7775 (mmm160) REVERT: C 215 GLU cc_start: 0.8263 (mp0) cc_final: 0.7627 (mp0) REVERT: C 217 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7895 (ppp) REVERT: D 20 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7707 (mtpm) REVERT: D 46 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8226 (mptt) REVERT: E 76 LYS cc_start: 0.8170 (ptpp) cc_final: 0.7572 (pttt) REVERT: A 613 VAL cc_start: 0.7793 (OUTLIER) cc_final: 0.7555 (t) REVERT: A 621 TYR cc_start: 0.4375 (OUTLIER) cc_final: 0.3190 (m-80) REVERT: A 780 MET cc_start: 0.4604 (mmm) cc_final: 0.2568 (tpp) REVERT: A 803 ILE cc_start: 0.8015 (mt) cc_final: 0.7640 (tp) outliers start: 43 outliers final: 21 residues processed: 156 average time/residue: 0.4750 time to fit residues: 79.4292 Evaluate side-chains 148 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 765 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN C 239 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.161154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119890 restraints weight = 9505.658| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.98 r_work: 0.3349 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8131 Z= 0.134 Angle : 0.507 7.751 11015 Z= 0.263 Chirality : 0.042 0.168 1240 Planarity : 0.004 0.040 1407 Dihedral : 5.057 49.801 1117 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.15 % Allowed : 26.07 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.20 (0.26), residues: 1001 helix: 2.68 (0.26), residues: 386 sheet: -0.49 (0.35), residues: 208 loop : -0.30 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.012 0.001 TYR E 80 PHE 0.011 0.001 PHE C 151 TRP 0.012 0.001 TRP B 100 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8129) covalent geometry : angle 0.50693 (11011) SS BOND : bond 0.00196 ( 2) SS BOND : angle 0.91848 ( 4) hydrogen bonds : bond 0.03424 ( 416) hydrogen bonds : angle 4.14247 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7721 (m-30) cc_final: 0.7063 (m-30) REVERT: B 55 LYS cc_start: 0.7047 (mptt) cc_final: 0.6204 (mtpt) REVERT: B 74 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: B 77 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8222 (ttmm) REVERT: B 82 LYS cc_start: 0.7465 (mmpt) cc_final: 0.6753 (ttmt) REVERT: B 95 ASP cc_start: 0.7468 (p0) cc_final: 0.7249 (p0) REVERT: B 118 ASP cc_start: 0.7862 (t0) cc_final: 0.7494 (t0) REVERT: B 124 GLU cc_start: 0.8108 (tt0) cc_final: 0.7470 (tp30) REVERT: B 148 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8573 (m110) REVERT: B 161 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7764 (mttt) REVERT: B 167 TYR cc_start: 0.8251 (m-80) cc_final: 0.7813 (m-80) REVERT: C 65 THR cc_start: 0.8432 (m) cc_final: 0.8185 (p) REVERT: C 76 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8409 (p0) REVERT: C 197 ARG cc_start: 0.8306 (mtp-110) cc_final: 0.7673 (mtm-85) REVERT: C 214 ARG cc_start: 0.8057 (mmt-90) cc_final: 0.7817 (mmm160) REVERT: C 215 GLU cc_start: 0.8288 (mp0) cc_final: 0.7722 (mp0) REVERT: C 217 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7913 (ppp) REVERT: C 333 ASP cc_start: 0.8812 (p0) cc_final: 0.8535 (p0) REVERT: D 20 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7852 (mtpm) REVERT: E 76 LYS cc_start: 0.8132 (ptpp) cc_final: 0.7569 (pttt) REVERT: A 613 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7613 (t) REVERT: A 758 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7835 (mm-30) REVERT: A 780 MET cc_start: 0.4661 (mmm) cc_final: 0.2630 (tpp) REVERT: A 803 ILE cc_start: 0.8075 (mt) cc_final: 0.7847 (mp) outliers start: 36 outliers final: 21 residues processed: 148 average time/residue: 0.5119 time to fit residues: 80.7048 Evaluate side-chains 146 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 765 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 94 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 84 optimal weight: 8.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN C 237 ASN C 239 ASN E 31 ASN E 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.164905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122295 restraints weight = 9571.114| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.11 r_work: 0.3356 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8131 Z= 0.112 Angle : 0.492 8.138 11015 Z= 0.254 Chirality : 0.042 0.173 1240 Planarity : 0.003 0.041 1407 Dihedral : 4.742 49.518 1115 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.50 % Allowed : 25.95 % Favored : 69.55 % 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: 1.33 (0.26), residues: 1001 helix: 2.77 (0.26), residues: 388 sheet: -0.41 (0.35), residues: 207 loop : -0.24 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.009 0.001 TYR A 834 PHE 0.013 0.001 PHE A 743 TRP 0.011 0.001 TRP B 100 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8129) covalent geometry : angle 0.49208 (11011) SS BOND : bond 0.00130 ( 2) SS BOND : angle 0.74655 ( 4) hydrogen bonds : bond 0.03242 ( 416) hydrogen bonds : angle 4.02345 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7676 (m-30) cc_final: 0.7000 (m-30) REVERT: B 55 LYS cc_start: 0.6953 (mptt) cc_final: 0.6088 (mtpt) REVERT: B 74 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: B 82 LYS cc_start: 0.7511 (mmpt) cc_final: 0.6821 (ttmt) REVERT: B 95 ASP cc_start: 0.7420 (p0) cc_final: 0.7189 (p0) REVERT: B 118 ASP cc_start: 0.7825 (t0) cc_final: 0.7431 (t0) REVERT: B 124 GLU cc_start: 0.8134 (tt0) cc_final: 0.7421 (tp30) REVERT: B 148 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8409 (m110) REVERT: B 161 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7719 (mttt) REVERT: B 167 TYR cc_start: 0.8146 (m-80) cc_final: 0.7710 (m-80) REVERT: C 65 THR cc_start: 0.8365 (m) cc_final: 0.8104 (p) REVERT: C 76 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8386 (p0) REVERT: C 197 ARG cc_start: 0.8271 (mtp-110) cc_final: 0.7607 (mtm-85) REVERT: C 214 ARG cc_start: 0.8033 (mmt-90) cc_final: 0.7780 (mmm160) REVERT: C 215 GLU cc_start: 0.8247 (mp0) cc_final: 0.7627 (mp0) REVERT: D 20 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7781 (mtpm) REVERT: D 26 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: E 76 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7473 (pttt) REVERT: A 613 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7549 (t) REVERT: A 758 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7762 (mm-30) outliers start: 39 outliers final: 20 residues processed: 153 average time/residue: 0.5076 time to fit residues: 83.2743 Evaluate side-chains 147 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 765 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 71 optimal weight: 0.0010 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN C 237 ASN E 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.163824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121739 restraints weight = 9612.673| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.10 r_work: 0.3350 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8131 Z= 0.125 Angle : 0.505 8.709 11015 Z= 0.260 Chirality : 0.042 0.178 1240 Planarity : 0.003 0.040 1407 Dihedral : 4.763 49.517 1115 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.96 % Allowed : 25.26 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.35 (0.26), residues: 1001 helix: 2.80 (0.26), residues: 387 sheet: -0.41 (0.35), residues: 208 loop : -0.23 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.013 0.001 TYR E 80 PHE 0.010 0.001 PHE C 151 TRP 0.011 0.001 TRP B 100 HIS 0.006 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8129) covalent geometry : angle 0.50504 (11011) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.75829 ( 4) hydrogen bonds : bond 0.03274 ( 416) hydrogen bonds : angle 4.01061 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7691 (m-30) cc_final: 0.7019 (m-30) REVERT: B 55 LYS cc_start: 0.6965 (mptt) cc_final: 0.6104 (mtpt) REVERT: B 74 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7075 (m-80) REVERT: B 82 LYS cc_start: 0.7510 (mmpt) cc_final: 0.6814 (ttmt) REVERT: B 95 ASP cc_start: 0.7427 (p0) cc_final: 0.7200 (p0) REVERT: B 118 ASP cc_start: 0.7843 (t0) cc_final: 0.7444 (t0) REVERT: B 124 GLU cc_start: 0.8115 (tt0) cc_final: 0.7428 (tp30) REVERT: B 128 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8127 (t0) REVERT: B 148 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8529 (m110) REVERT: B 161 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7706 (mttt) REVERT: B 167 TYR cc_start: 0.8146 (m-80) cc_final: 0.7723 (m-80) REVERT: B 210 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6458 (m-30) REVERT: C 19 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7435 (ttm110) REVERT: C 65 THR cc_start: 0.8372 (m) cc_final: 0.8109 (p) REVERT: C 76 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8412 (p0) REVERT: C 197 ARG cc_start: 0.8284 (mtp-110) cc_final: 0.7616 (mtm-85) REVERT: C 214 ARG cc_start: 0.8031 (mmt-90) cc_final: 0.7776 (mmm160) REVERT: C 215 GLU cc_start: 0.8224 (mp0) cc_final: 0.7601 (mp0) REVERT: D 20 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7785 (mtpm) REVERT: D 26 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: D 46 LYS cc_start: 0.8051 (mptt) cc_final: 0.7823 (mmtt) REVERT: E 76 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7495 (pttt) REVERT: A 613 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7555 (t) REVERT: A 685 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7310 (tp) REVERT: A 758 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7744 (mm-30) outliers start: 43 outliers final: 23 residues processed: 153 average time/residue: 0.4897 time to fit residues: 80.2103 Evaluate side-chains 153 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 765 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN C 237 ASN E 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116222 restraints weight = 9540.981| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.21 r_work: 0.3258 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8131 Z= 0.127 Angle : 0.507 8.643 11015 Z= 0.260 Chirality : 0.042 0.187 1240 Planarity : 0.003 0.040 1407 Dihedral : 4.770 49.659 1115 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.19 % Allowed : 25.61 % Favored : 69.20 % 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: 1.38 (0.27), residues: 1001 helix: 2.76 (0.25), residues: 390 sheet: -0.44 (0.35), residues: 214 loop : -0.12 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.010 0.001 TYR B 195 PHE 0.025 0.001 PHE A 684 TRP 0.011 0.001 TRP B 100 HIS 0.006 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8129) covalent geometry : angle 0.50666 (11011) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.76354 ( 4) hydrogen bonds : bond 0.03270 ( 416) hydrogen bonds : angle 3.99356 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7610 (m-30) cc_final: 0.6904 (m-30) REVERT: B 55 LYS cc_start: 0.6772 (mptt) cc_final: 0.5949 (mtpt) REVERT: B 74 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.6929 (m-80) REVERT: B 75 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: B 77 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7885 (ttmm) REVERT: B 82 LYS cc_start: 0.7502 (mmpt) cc_final: 0.6803 (ttmt) REVERT: B 95 ASP cc_start: 0.7418 (p0) cc_final: 0.7187 (p0) REVERT: B 118 ASP cc_start: 0.7750 (t0) cc_final: 0.7305 (t0) REVERT: B 124 GLU cc_start: 0.8130 (tt0) cc_final: 0.7381 (tp30) REVERT: B 128 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8106 (t0) REVERT: B 148 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8509 (m110) REVERT: B 161 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7675 (mttt) REVERT: B 167 TYR cc_start: 0.8031 (m-80) cc_final: 0.7589 (m-80) REVERT: B 210 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6432 (m-30) REVERT: C 65 THR cc_start: 0.8314 (m) cc_final: 0.8035 (p) REVERT: C 76 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8440 (p0) REVERT: C 197 ARG cc_start: 0.8291 (mtp-110) cc_final: 0.7592 (mtm-85) REVERT: C 214 ARG cc_start: 0.8038 (mmt-90) cc_final: 0.7757 (mmm160) REVERT: C 215 GLU cc_start: 0.8223 (mp0) cc_final: 0.7544 (mp0) REVERT: D 20 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7776 (mtpm) REVERT: D 26 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8184 (m-30) REVERT: D 46 LYS cc_start: 0.8009 (mptt) cc_final: 0.7763 (mmtt) REVERT: E 76 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7450 (pttt) REVERT: A 613 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7529 (t) REVERT: A 685 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7236 (tp) REVERT: A 758 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7803 (mm-30) outliers start: 45 outliers final: 25 residues processed: 159 average time/residue: 0.4945 time to fit residues: 84.4483 Evaluate side-chains 159 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 765 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 18 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 89 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 0.0570 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN E 31 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118029 restraints weight = 9478.903| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.06 r_work: 0.3279 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8131 Z= 0.108 Angle : 0.499 8.612 11015 Z= 0.256 Chirality : 0.041 0.192 1240 Planarity : 0.003 0.040 1407 Dihedral : 4.727 49.885 1115 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.27 % Allowed : 26.87 % Favored : 68.86 % 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: 1.43 (0.27), residues: 1001 helix: 2.79 (0.26), residues: 390 sheet: -0.37 (0.35), residues: 211 loop : -0.11 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 19 TYR 0.012 0.001 TYR E 80 PHE 0.010 0.001 PHE C 199 TRP 0.011 0.001 TRP B 100 HIS 0.006 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8129) covalent geometry : angle 0.49903 (11011) SS BOND : bond 0.00109 ( 2) SS BOND : angle 0.62254 ( 4) hydrogen bonds : bond 0.03160 ( 416) hydrogen bonds : angle 3.94909 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7629 (m-30) cc_final: 0.6933 (m-30) REVERT: B 55 LYS cc_start: 0.6782 (mptt) cc_final: 0.5948 (mtpt) REVERT: B 74 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: B 77 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7826 (ttmm) REVERT: B 82 LYS cc_start: 0.7490 (mmpt) cc_final: 0.6829 (ttmt) REVERT: B 95 ASP cc_start: 0.7422 (p0) cc_final: 0.7181 (p0) REVERT: B 118 ASP cc_start: 0.7733 (t0) cc_final: 0.7311 (t0) REVERT: B 124 GLU cc_start: 0.8054 (tt0) cc_final: 0.7380 (tp30) REVERT: B 148 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8427 (m110) REVERT: B 161 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7647 (mttt) REVERT: B 167 TYR cc_start: 0.8091 (m-80) cc_final: 0.7608 (m-80) REVERT: B 210 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6448 (m-30) REVERT: C 19 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7382 (ttm110) REVERT: C 76 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8418 (p0) REVERT: C 197 ARG cc_start: 0.8270 (mtp-110) cc_final: 0.7567 (mtm-85) REVERT: C 214 ARG cc_start: 0.8022 (mmt-90) cc_final: 0.7754 (mmm160) REVERT: C 215 GLU cc_start: 0.8220 (mp0) cc_final: 0.7554 (mp0) REVERT: D 20 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7734 (mtpm) REVERT: D 26 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: E 76 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7391 (pttt) REVERT: A 613 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7506 (t) REVERT: A 685 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7249 (tp) REVERT: A 758 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7786 (mm-30) outliers start: 37 outliers final: 21 residues processed: 152 average time/residue: 0.5029 time to fit residues: 81.8147 Evaluate side-chains 154 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 765 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 76 optimal weight: 0.0040 chunk 95 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 148 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.158520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118779 restraints weight = 9449.439| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.06 r_work: 0.3290 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8131 Z= 0.101 Angle : 0.492 9.080 11015 Z= 0.254 Chirality : 0.041 0.194 1240 Planarity : 0.003 0.040 1407 Dihedral : 4.678 49.836 1115 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.69 % Allowed : 27.57 % Favored : 68.74 % 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: 1.47 (0.27), residues: 1001 helix: 2.85 (0.26), residues: 388 sheet: -0.33 (0.35), residues: 211 loop : -0.11 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 19 TYR 0.009 0.001 TYR A 834 PHE 0.010 0.001 PHE C 199 TRP 0.012 0.001 TRP B 100 HIS 0.005 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8129) covalent geometry : angle 0.49238 (11011) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.57517 ( 4) hydrogen bonds : bond 0.03095 ( 416) hydrogen bonds : angle 3.89851 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7617 (m-30) cc_final: 0.6912 (m-30) REVERT: B 55 LYS cc_start: 0.6810 (mptt) cc_final: 0.5955 (mtpt) REVERT: B 74 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: B 77 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7882 (ttmm) REVERT: B 82 LYS cc_start: 0.7506 (mmpt) cc_final: 0.6844 (ttmt) REVERT: B 95 ASP cc_start: 0.7397 (p0) cc_final: 0.7171 (p0) REVERT: B 118 ASP cc_start: 0.7673 (t0) cc_final: 0.7263 (t0) REVERT: B 124 GLU cc_start: 0.8070 (tt0) cc_final: 0.7357 (tp30) REVERT: B 148 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8413 (m110) REVERT: B 161 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7634 (mttt) REVERT: B 167 TYR cc_start: 0.8083 (m-80) cc_final: 0.7605 (m-80) REVERT: B 210 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6432 (m-30) REVERT: C 19 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7376 (ttm110) REVERT: C 76 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8436 (p0) REVERT: C 197 ARG cc_start: 0.8252 (mtp-110) cc_final: 0.7560 (mtm-85) REVERT: C 214 ARG cc_start: 0.8007 (mmt-90) cc_final: 0.7738 (mmm160) REVERT: C 215 GLU cc_start: 0.8205 (mp0) cc_final: 0.7536 (mp0) REVERT: D 20 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7709 (mtpm) REVERT: D 26 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: E 76 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7367 (pttt) REVERT: A 613 VAL cc_start: 0.7719 (OUTLIER) cc_final: 0.7480 (t) REVERT: A 685 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7254 (tp) REVERT: A 758 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7778 (mm-30) outliers start: 32 outliers final: 20 residues processed: 152 average time/residue: 0.5174 time to fit residues: 84.0758 Evaluate side-chains 152 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 765 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN C 237 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117803 restraints weight = 9506.047| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.07 r_work: 0.3277 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8131 Z= 0.121 Angle : 0.504 9.223 11015 Z= 0.260 Chirality : 0.042 0.193 1240 Planarity : 0.003 0.040 1407 Dihedral : 4.714 49.910 1115 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.69 % Allowed : 28.14 % Favored : 68.17 % 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: 1.42 (0.27), residues: 1001 helix: 2.81 (0.26), residues: 388 sheet: -0.37 (0.35), residues: 212 loop : -0.13 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.013 0.001 TYR E 80 PHE 0.010 0.001 PHE C 151 TRP 0.010 0.001 TRP B 100 HIS 0.005 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8129) covalent geometry : angle 0.50395 (11011) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.71665 ( 4) hydrogen bonds : bond 0.03177 ( 416) hydrogen bonds : angle 3.91270 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.95 seconds wall clock time: 51 minutes 30.93 seconds (3090.93 seconds total)