Starting phenix.real_space_refine on Fri Jun 6 16:37:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nox_49620/06_2025/9nox_49620.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nox_49620/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9nox_49620/06_2025/9nox_49620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nox_49620/06_2025/9nox_49620.map" model { file = "/net/cci-nas-00/data/ceres_data/9nox_49620/06_2025/9nox_49620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nox_49620/06_2025/9nox_49620.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.30, per 1000 atoms: 0.79 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: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.07 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: 2.58 Time building geometry restraints manager: 2.35 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: 61.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.420 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (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 TRP 0.009 0.001 TRP B 100 HIS 0.004 0.001 HIS B 213 PHE 0.023 0.001 PHE A 761 TYR 0.013 0.001 TYR A 621 ARG 0.009 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.16061 ( 416) hydrogen bonds : angle 6.11838 ( 1191) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.54888 ( 4) covalent geometry : bond 0.00262 ( 8129) covalent geometry : angle 0.52187 (11011) *********************** 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 : 0.917 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: 1.1505 time to fit residues: 161.0708 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 : 0.898 ------------------------------------------------------------------------------- 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 82 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.163168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119111 restraints weight = 9554.226| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.26 r_work: 0.3304 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8131 Z= 0.166 Angle : 0.538 7.145 11015 Z= 0.280 Chirality : 0.043 0.141 1240 Planarity : 0.004 0.040 1407 Dihedral : 6.419 59.693 1136 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.92 % Allowed : 26.18 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1001 helix: 2.36 (0.26), residues: 390 sheet: -0.43 (0.35), residues: 214 loop : -0.34 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 100 HIS 0.005 0.001 HIS B 213 PHE 0.013 0.001 PHE A 761 TYR 0.012 0.001 TYR B 195 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 416) hydrogen bonds : angle 4.54457 ( 1191) SS BOND : bond 0.00341 ( 2) SS BOND : angle 1.31820 ( 4) covalent geometry : bond 0.00392 ( 8129) covalent geometry : angle 0.53797 (11011) *********************** 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 159 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7720 (m-30) cc_final: 0.7066 (m-30) REVERT: B 55 LYS cc_start: 0.6974 (mptt) cc_final: 0.6085 (mtpt) REVERT: B 74 PHE cc_start: 0.7719 (t80) cc_final: 0.7034 (m-80) REVERT: B 95 ASP cc_start: 0.7480 (p0) cc_final: 0.7249 (p0) REVERT: B 124 GLU cc_start: 0.8136 (tt0) cc_final: 0.7486 (tp30) REVERT: B 167 TYR cc_start: 0.8146 (m-80) cc_final: 0.7664 (m-80) REVERT: B 170 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7954 (pt0) REVERT: C 65 THR cc_start: 0.8410 (m) cc_final: 0.8154 (p) REVERT: C 197 ARG cc_start: 0.8223 (mtp-110) cc_final: 0.7544 (mtm-85) REVERT: C 214 ARG cc_start: 0.8011 (mmt-90) cc_final: 0.7736 (mmm160) REVERT: C 215 GLU cc_start: 0.8230 (mp0) cc_final: 0.7613 (mp0) REVERT: C 217 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7865 (ppp) REVERT: D 20 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7687 (mtpm) REVERT: D 46 LYS cc_start: 0.8491 (mmmt) cc_final: 0.8223 (mptt) REVERT: E 76 LYS cc_start: 0.8179 (ptpp) cc_final: 0.7573 (pttt) REVERT: A 621 TYR cc_start: 0.4203 (OUTLIER) cc_final: 0.3080 (m-80) REVERT: A 780 MET cc_start: 0.4435 (mmm) cc_final: 0.2575 (tpp) REVERT: A 803 ILE cc_start: 0.7903 (mp) cc_final: 0.7681 (tp) outliers start: 34 outliers final: 14 residues processed: 148 average time/residue: 1.1476 time to fit residues: 182.5718 Evaluate side-chains 137 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 17 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 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 765 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 84 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 90 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.162790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119281 restraints weight = 9595.459| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.23 r_work: 0.3299 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8131 Z= 0.159 Angle : 0.527 8.567 11015 Z= 0.273 Chirality : 0.043 0.157 1240 Planarity : 0.004 0.041 1407 Dihedral : 5.246 51.127 1118 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.65 % Allowed : 25.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1001 helix: 2.53 (0.26), residues: 385 sheet: -0.53 (0.34), residues: 221 loop : -0.31 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 100 HIS 0.005 0.001 HIS B 213 PHE 0.024 0.001 PHE A 684 TYR 0.015 0.001 TYR E 80 ARG 0.006 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 416) hydrogen bonds : angle 4.32311 ( 1191) SS BOND : bond 0.00188 ( 2) SS BOND : angle 1.36819 ( 4) covalent geometry : bond 0.00379 ( 8129) covalent geometry : angle 0.52690 (11011) *********************** 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 173 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 0.842 Fit side-chains REVERT: B 30 ASP cc_start: 0.7686 (m-30) cc_final: 0.7020 (m-30) REVERT: B 55 LYS cc_start: 0.6972 (mptt) cc_final: 0.6077 (mtpt) REVERT: B 74 PHE cc_start: 0.7759 (t80) cc_final: 0.7069 (m-80) REVERT: B 95 ASP cc_start: 0.7491 (p0) cc_final: 0.7253 (p0) REVERT: B 124 GLU cc_start: 0.8125 (tt0) cc_final: 0.7425 (tp30) REVERT: B 148 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8507 (m110) REVERT: B 161 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7762 (mttt) REVERT: B 167 TYR cc_start: 0.8191 (m-80) cc_final: 0.7704 (m-80) REVERT: B 170 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7989 (pt0) REVERT: C 197 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7568 (mtm-85) REVERT: C 214 ARG cc_start: 0.8038 (mmt-90) cc_final: 0.7769 (mmm160) REVERT: C 215 GLU cc_start: 0.8261 (mp0) cc_final: 0.7643 (mp0) REVERT: C 217 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7894 (ppp) REVERT: D 20 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7748 (mtpm) REVERT: D 46 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8236 (mptt) REVERT: E 76 LYS cc_start: 0.8179 (ptpp) cc_final: 0.7579 (pttt) REVERT: A 613 VAL cc_start: 0.7816 (OUTLIER) cc_final: 0.7589 (t) REVERT: A 621 TYR cc_start: 0.4352 (OUTLIER) cc_final: 0.3183 (m-80) REVERT: A 780 MET cc_start: 0.4600 (mmm) cc_final: 0.2601 (tpp) REVERT: A 803 ILE cc_start: 0.7993 (mt) cc_final: 0.7671 (tp) outliers start: 49 outliers final: 23 residues processed: 160 average time/residue: 1.0198 time to fit residues: 174.8509 Evaluate side-chains 148 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 32 GLN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 189 SER 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 17 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 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 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 94 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 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 = 0.3968 r_free = 0.3968 target = 0.162943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119313 restraints weight = 9555.450| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.24 r_work: 0.3312 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8131 Z= 0.127 Angle : 0.503 7.628 11015 Z= 0.261 Chirality : 0.042 0.157 1240 Planarity : 0.003 0.040 1407 Dihedral : 5.199 50.366 1118 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.07 % Allowed : 25.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.27), residues: 1001 helix: 2.64 (0.26), residues: 386 sheet: -0.55 (0.35), residues: 214 loop : -0.30 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 100 HIS 0.004 0.001 HIS B 213 PHE 0.011 0.001 PHE C 199 TYR 0.010 0.001 TYR A 834 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 416) hydrogen bonds : angle 4.21394 ( 1191) SS BOND : bond 0.00178 ( 2) SS BOND : angle 1.27461 ( 4) covalent geometry : bond 0.00295 ( 8129) covalent geometry : angle 0.50251 (11011) *********************** 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 168 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.905 Fit side-chains REVERT: B 30 ASP cc_start: 0.7667 (m-30) cc_final: 0.6988 (m-30) REVERT: B 55 LYS cc_start: 0.6971 (mptt) cc_final: 0.6088 (mtpt) REVERT: B 74 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7031 (m-80) REVERT: B 77 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8156 (ttmm) REVERT: B 95 ASP cc_start: 0.7446 (p0) cc_final: 0.7210 (p0) REVERT: B 118 ASP cc_start: 0.7805 (t0) cc_final: 0.7395 (t0) REVERT: B 124 GLU cc_start: 0.8116 (tt0) cc_final: 0.7407 (tp30) REVERT: B 148 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8588 (m110) REVERT: B 161 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7760 (mttt) REVERT: B 167 TYR cc_start: 0.8153 (m-80) cc_final: 0.7677 (m-80) REVERT: B 170 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7972 (pt0) REVERT: C 65 THR cc_start: 0.8458 (m) cc_final: 0.8179 (p) REVERT: C 76 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8440 (p0) REVERT: C 197 ARG cc_start: 0.8272 (mtp-110) cc_final: 0.7558 (mtm-85) REVERT: C 214 ARG cc_start: 0.8023 (mmt-90) cc_final: 0.7745 (mmm160) REVERT: C 215 GLU cc_start: 0.8213 (mp0) cc_final: 0.7571 (mp0) REVERT: C 217 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7885 (ppp) REVERT: D 20 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7739 (mtpm) REVERT: D 46 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8220 (mptt) REVERT: E 76 LYS cc_start: 0.8110 (ptpp) cc_final: 0.7499 (pttt) REVERT: A 613 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7571 (t) REVERT: A 621 TYR cc_start: 0.4389 (OUTLIER) cc_final: 0.3148 (m-80) REVERT: A 758 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7852 (mm-30) REVERT: A 780 MET cc_start: 0.4625 (mmm) cc_final: 0.2563 (tpp) REVERT: A 803 ILE cc_start: 0.8007 (mt) cc_final: 0.7787 (mp) outliers start: 44 outliers final: 19 residues processed: 155 average time/residue: 0.9930 time to fit residues: 164.8992 Evaluate side-chains 144 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 87 THR Chi-restraints excluded: chain C residue 189 SER 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 4 LEU 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 788 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118644 restraints weight = 9511.045| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.23 r_work: 0.3301 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1223 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= 0.149 Angle : 0.514 7.690 11015 Z= 0.267 Chirality : 0.043 0.172 1240 Planarity : 0.004 0.041 1407 Dihedral : 5.105 50.150 1117 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.77 % Allowed : 24.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1001 helix: 2.62 (0.26), residues: 386 sheet: -0.55 (0.35), residues: 214 loop : -0.32 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 100 HIS 0.004 0.001 HIS B 213 PHE 0.011 0.001 PHE C 151 TYR 0.013 0.001 TYR E 80 ARG 0.002 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 416) hydrogen bonds : angle 4.17071 ( 1191) SS BOND : bond 0.00216 ( 2) SS BOND : angle 1.05371 ( 4) covalent geometry : bond 0.00353 ( 8129) covalent geometry : angle 0.51378 (11011) *********************** 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 175 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.869 Fit side-chains REVERT: B 21 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6808 (ttpp) REVERT: B 30 ASP cc_start: 0.7706 (m-30) cc_final: 0.7018 (m-30) REVERT: B 55 LYS cc_start: 0.6951 (mptt) cc_final: 0.6097 (mtpt) REVERT: B 74 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7047 (m-80) REVERT: B 77 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8208 (ttmm) REVERT: B 118 ASP cc_start: 0.7850 (t0) cc_final: 0.7443 (t0) REVERT: B 124 GLU cc_start: 0.8123 (tt0) cc_final: 0.7442 (tp30) REVERT: B 148 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8542 (m110) REVERT: B 161 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7758 (mttt) REVERT: B 167 TYR cc_start: 0.8187 (m-80) cc_final: 0.7729 (m-80) REVERT: B 170 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8006 (pt0) REVERT: C 65 THR cc_start: 0.8491 (m) cc_final: 0.8217 (p) REVERT: C 76 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8455 (p0) REVERT: C 197 ARG cc_start: 0.8300 (mtp-110) cc_final: 0.7601 (mtm-85) REVERT: C 214 ARG cc_start: 0.8061 (mmt-90) cc_final: 0.7795 (mmm160) REVERT: C 215 GLU cc_start: 0.8267 (mp0) cc_final: 0.7651 (mp0) REVERT: C 217 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7948 (ppp) REVERT: D 20 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7810 (mtpm) REVERT: D 26 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8227 (m-30) REVERT: D 46 LYS cc_start: 0.8487 (mmmt) cc_final: 0.8250 (mptt) REVERT: E 76 LYS cc_start: 0.8145 (ptpp) cc_final: 0.7542 (pttt) REVERT: A 613 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7622 (t) REVERT: A 685 ILE cc_start: 0.7588 (mm) cc_final: 0.7378 (tp) REVERT: A 758 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7839 (mm-30) REVERT: A 780 MET cc_start: 0.4728 (mmm) cc_final: 0.2694 (tpp) REVERT: A 803 ILE cc_start: 0.8053 (mt) cc_final: 0.7811 (mp) REVERT: A 823 THR cc_start: 0.7562 (m) cc_final: 0.7349 (p) outliers start: 50 outliers final: 29 residues processed: 160 average time/residue: 0.9568 time to fit residues: 164.5596 Evaluate side-chains 157 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 21 LYS 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 173 ARG 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 189 SER Chi-restraints excluded: chain C residue 217 MET 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 17 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 61 THR 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 620 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 Chi-restraints excluded: chain A residue 788 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.163672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121050 restraints weight = 9557.834| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.11 r_work: 0.3325 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8131 Z= 0.130 Angle : 0.505 7.969 11015 Z= 0.262 Chirality : 0.042 0.173 1240 Planarity : 0.004 0.041 1407 Dihedral : 4.858 50.170 1115 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.19 % Allowed : 24.91 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1001 helix: 2.69 (0.26), residues: 387 sheet: -0.52 (0.35), residues: 214 loop : -0.28 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 100 HIS 0.004 0.001 HIS B 213 PHE 0.011 0.001 PHE C 151 TYR 0.010 0.001 TYR B 195 ARG 0.006 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 416) hydrogen bonds : angle 4.11954 ( 1191) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.86072 ( 4) covalent geometry : bond 0.00304 ( 8129) covalent geometry : angle 0.50511 (11011) *********************** 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 174 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.949 Fit side-chains REVERT: B 21 LYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6811 (ttpp) REVERT: B 30 ASP cc_start: 0.7681 (m-30) cc_final: 0.6998 (m-30) REVERT: B 55 LYS cc_start: 0.6971 (mptt) cc_final: 0.6132 (mtpt) REVERT: B 57 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7168 (mtp) REVERT: B 74 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7020 (m-80) REVERT: B 77 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8206 (ttmm) REVERT: B 118 ASP cc_start: 0.7830 (t0) cc_final: 0.7437 (t0) REVERT: B 124 GLU cc_start: 0.8078 (tt0) cc_final: 0.7430 (tp30) REVERT: B 148 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8598 (m110) REVERT: B 161 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7770 (mttt) REVERT: B 167 TYR cc_start: 0.8188 (m-80) cc_final: 0.7748 (m-80) REVERT: B 170 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8022 (pt0) REVERT: C 65 THR cc_start: 0.8458 (m) cc_final: 0.8195 (p) REVERT: C 76 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8421 (p0) REVERT: C 197 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.7596 (mtm-85) REVERT: C 214 ARG cc_start: 0.8038 (mmt-90) cc_final: 0.7786 (mmm160) REVERT: C 215 GLU cc_start: 0.8272 (mp0) cc_final: 0.7662 (mp0) REVERT: D 20 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7831 (mtpm) REVERT: D 26 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8214 (m-30) REVERT: D 46 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8251 (mptt) REVERT: E 76 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7530 (pttt) REVERT: A 613 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7624 (t) REVERT: A 633 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.4830 (ttm170) REVERT: A 685 ILE cc_start: 0.7582 (mm) cc_final: 0.7367 (tp) REVERT: A 758 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7753 (mm-30) outliers start: 45 outliers final: 26 residues processed: 159 average time/residue: 0.9958 time to fit residues: 169.9842 Evaluate side-chains 158 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 21 LYS Chi-restraints excluded: chain B residue 57 MET 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 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 189 SER 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 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 620 VAL Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 788 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.154984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115079 restraints weight = 9528.358| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.06 r_work: 0.3236 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1388 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= 0.164 Angle : 0.532 8.846 11015 Z= 0.275 Chirality : 0.043 0.181 1240 Planarity : 0.004 0.041 1407 Dihedral : 4.932 50.244 1115 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 6.57 % Allowed : 23.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1001 helix: 2.62 (0.25), residues: 387 sheet: -0.54 (0.35), residues: 214 loop : -0.28 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 100 HIS 0.005 0.001 HIS B 213 PHE 0.025 0.001 PHE A 684 TYR 0.015 0.001 TYR E 80 ARG 0.003 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 416) hydrogen bonds : angle 4.14261 ( 1191) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.97471 ( 4) covalent geometry : bond 0.00391 ( 8129) covalent geometry : angle 0.53218 (11011) *********************** 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 182 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 125 time to evaluate : 0.829 Fit side-chains REVERT: B 21 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6676 (ttpp) REVERT: B 30 ASP cc_start: 0.7674 (m-30) cc_final: 0.6975 (m-30) REVERT: B 55 LYS cc_start: 0.6770 (mptt) cc_final: 0.5933 (mtpt) REVERT: B 57 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7124 (mtp) REVERT: B 74 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: B 77 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8192 (ttmm) REVERT: B 118 ASP cc_start: 0.7770 (t0) cc_final: 0.7333 (t0) REVERT: B 124 GLU cc_start: 0.8131 (tt0) cc_final: 0.7384 (tp30) REVERT: B 128 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8146 (t0) REVERT: B 148 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8529 (m110) REVERT: B 161 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7757 (mttt) REVERT: B 167 TYR cc_start: 0.8121 (m-80) cc_final: 0.7629 (m-80) REVERT: B 170 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7972 (pt0) REVERT: B 210 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6482 (m-30) REVERT: C 65 THR cc_start: 0.8450 (m) cc_final: 0.8137 (p) REVERT: C 76 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8499 (p0) REVERT: C 130 GLU cc_start: 0.4508 (mp0) cc_final: 0.4266 (pm20) REVERT: C 197 ARG cc_start: 0.8337 (mtp-110) cc_final: 0.7606 (mtm-85) REVERT: C 214 ARG cc_start: 0.8046 (mmt-90) cc_final: 0.7772 (mmm160) REVERT: C 215 GLU cc_start: 0.8259 (mp0) cc_final: 0.7608 (mp0) REVERT: D 20 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7817 (mtpm) REVERT: D 26 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8224 (m-30) REVERT: D 46 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8207 (mptt) REVERT: E 76 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7547 (pttt) REVERT: A 613 VAL cc_start: 0.7834 (OUTLIER) cc_final: 0.7616 (t) REVERT: A 633 ARG cc_start: 0.6070 (OUTLIER) cc_final: 0.4805 (ttm170) REVERT: A 758 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7748 (mm-30) outliers start: 57 outliers final: 28 residues processed: 165 average time/residue: 0.9764 time to fit residues: 172.7896 Evaluate side-chains 162 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 21 LYS Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 57 MET 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 128 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 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 189 SER 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 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 620 VAL Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 788 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 89 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.154852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115015 restraints weight = 9538.794| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.06 r_work: 0.3235 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8131 Z= 0.161 Angle : 0.540 8.676 11015 Z= 0.278 Chirality : 0.043 0.165 1240 Planarity : 0.004 0.041 1407 Dihedral : 4.963 50.367 1115 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.65 % Allowed : 25.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1001 helix: 2.58 (0.25), residues: 389 sheet: -0.56 (0.35), residues: 214 loop : -0.27 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 100 HIS 0.005 0.001 HIS B 213 PHE 0.012 0.001 PHE C 151 TYR 0.011 0.001 TYR B 195 ARG 0.005 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 416) hydrogen bonds : angle 4.14419 ( 1191) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.94091 ( 4) covalent geometry : bond 0.00384 ( 8129) covalent geometry : angle 0.53933 (11011) *********************** 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 173 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 0.898 Fit side-chains REVERT: B 21 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6698 (ttpp) REVERT: B 30 ASP cc_start: 0.7648 (m-30) cc_final: 0.6980 (m-30) REVERT: B 55 LYS cc_start: 0.6637 (mptt) cc_final: 0.5824 (mtpt) REVERT: B 57 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7095 (mtp) REVERT: B 74 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: B 75 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: B 77 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8196 (ttmm) REVERT: B 118 ASP cc_start: 0.7769 (t0) cc_final: 0.7373 (t0) REVERT: B 124 GLU cc_start: 0.8141 (tt0) cc_final: 0.7396 (tp30) REVERT: B 128 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8129 (t0) REVERT: B 148 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8536 (m110) REVERT: B 161 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7757 (mttt) REVERT: B 167 TYR cc_start: 0.8125 (m-80) cc_final: 0.7644 (m-80) REVERT: B 170 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7995 (pt0) REVERT: B 210 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6493 (m-30) REVERT: C 19 ARG cc_start: 0.7810 (mtp-110) cc_final: 0.7387 (ttm110) REVERT: C 65 THR cc_start: 0.8460 (m) cc_final: 0.8144 (p) REVERT: C 76 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8470 (p0) REVERT: C 127 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7911 (mtpt) REVERT: C 130 GLU cc_start: 0.4513 (mp0) cc_final: 0.4263 (pm20) REVERT: C 197 ARG cc_start: 0.8326 (mtp-110) cc_final: 0.7594 (mtm-85) REVERT: C 214 ARG cc_start: 0.8026 (mmt-90) cc_final: 0.7762 (mmm160) REVERT: C 215 GLU cc_start: 0.8276 (mp0) cc_final: 0.7623 (mp0) REVERT: D 20 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7838 (mtpm) REVERT: D 26 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8232 (m-30) REVERT: D 31 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8007 (p) REVERT: D 46 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8206 (mptt) REVERT: E 76 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7549 (pttt) REVERT: A 633 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.4679 (ttm170) REVERT: A 685 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7165 (tp) REVERT: A 758 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7772 (mm-30) outliers start: 49 outliers final: 29 residues processed: 161 average time/residue: 1.0544 time to fit residues: 182.8105 Evaluate side-chains 167 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 21 LYS Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 57 MET 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 173 ARG 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 189 SER 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 D residue 31 SER 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 571 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115232 restraints weight = 9590.010| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.07 r_work: 0.3237 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1474 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= 0.151 Angle : 0.535 8.909 11015 Z= 0.276 Chirality : 0.043 0.163 1240 Planarity : 0.004 0.041 1407 Dihedral : 4.956 50.550 1115 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.42 % Allowed : 26.07 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1001 helix: 2.58 (0.25), residues: 390 sheet: -0.53 (0.35), residues: 214 loop : -0.27 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 100 HIS 0.004 0.001 HIS B 213 PHE 0.011 0.001 PHE C 151 TYR 0.015 0.001 TYR E 80 ARG 0.005 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 416) hydrogen bonds : angle 4.13419 ( 1191) SS BOND : bond 0.00234 ( 2) SS BOND : angle 1.20662 ( 4) covalent geometry : bond 0.00360 ( 8129) covalent geometry : angle 0.53418 (11011) *********************** 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 170 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 0.874 Fit side-chains REVERT: B 21 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6696 (ttpp) REVERT: B 30 ASP cc_start: 0.7662 (m-30) cc_final: 0.6976 (m-30) REVERT: B 55 LYS cc_start: 0.6663 (mptt) cc_final: 0.5835 (mtpt) REVERT: B 57 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.7103 (mtp) REVERT: B 74 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.6921 (m-80) REVERT: B 75 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: B 77 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8204 (ttmm) REVERT: B 118 ASP cc_start: 0.7758 (t0) cc_final: 0.7372 (t0) REVERT: B 124 GLU cc_start: 0.8142 (tt0) cc_final: 0.7398 (tp30) REVERT: B 128 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8140 (t0) REVERT: B 148 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8554 (m110) REVERT: B 161 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7740 (mttt) REVERT: B 167 TYR cc_start: 0.8120 (m-80) cc_final: 0.7646 (m-80) REVERT: B 170 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7967 (pt0) REVERT: B 210 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6490 (m-30) REVERT: C 65 THR cc_start: 0.8460 (m) cc_final: 0.8145 (p) REVERT: C 76 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8427 (p0) REVERT: C 130 GLU cc_start: 0.4496 (mp0) cc_final: 0.4242 (pm20) REVERT: C 197 ARG cc_start: 0.8325 (mtp-110) cc_final: 0.7592 (mtm-85) REVERT: C 214 ARG cc_start: 0.8026 (mmt-90) cc_final: 0.7763 (mmm160) REVERT: C 215 GLU cc_start: 0.8252 (mp0) cc_final: 0.7604 (mp0) REVERT: D 20 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7835 (mtpm) REVERT: D 26 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8199 (m-30) REVERT: D 31 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.7981 (p) REVERT: D 46 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8210 (mptt) REVERT: E 76 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7534 (pttt) REVERT: A 633 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.4712 (ttm170) REVERT: A 685 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7170 (tp) REVERT: A 758 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7802 (mm-30) outliers start: 47 outliers final: 28 residues processed: 159 average time/residue: 1.0588 time to fit residues: 179.7423 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 : 0.809 ------------------------------------------------------------------------------- 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 21 LYS Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 57 MET 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 173 ARG 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 189 SER 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 D residue 31 SER 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 620 VAL Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 788 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.155800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116039 restraints weight = 9512.470| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.07 r_work: 0.3253 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8131 Z= 0.128 Angle : 0.525 9.176 11015 Z= 0.270 Chirality : 0.042 0.160 1240 Planarity : 0.004 0.041 1407 Dihedral : 4.910 50.716 1115 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.07 % Allowed : 26.53 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 1001 helix: 2.61 (0.26), residues: 390 sheet: -0.50 (0.35), residues: 214 loop : -0.25 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 100 HIS 0.004 0.001 HIS B 213 PHE 0.011 0.001 PHE C 151 TYR 0.010 0.001 TYR B 195 ARG 0.006 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 416) hydrogen bonds : angle 4.08211 ( 1191) SS BOND : bond 0.00189 ( 2) SS BOND : angle 1.01948 ( 4) covalent geometry : bond 0.00299 ( 8129) covalent geometry : angle 0.52455 (11011) ********************** 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 166 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.893 Fit side-chains REVERT: B 21 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6683 (ttpp) REVERT: B 30 ASP cc_start: 0.7617 (m-30) cc_final: 0.6928 (m-30) REVERT: B 55 LYS cc_start: 0.6642 (mptt) cc_final: 0.5822 (mtpt) REVERT: B 57 MET cc_start: 0.7320 (ttm) cc_final: 0.7085 (mtp) REVERT: B 74 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: B 77 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8171 (ttmm) REVERT: B 118 ASP cc_start: 0.7761 (t0) cc_final: 0.7375 (t0) REVERT: B 124 GLU cc_start: 0.8134 (tt0) cc_final: 0.7389 (tp30) REVERT: B 148 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8516 (m110) REVERT: B 161 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7716 (mttt) REVERT: B 167 TYR cc_start: 0.8112 (m-80) cc_final: 0.7644 (m-80) REVERT: B 170 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7961 (pt0) REVERT: B 210 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6483 (m-30) REVERT: B 214 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7873 (t80) REVERT: C 19 ARG cc_start: 0.7818 (mtp-110) cc_final: 0.7416 (ttm110) REVERT: C 65 THR cc_start: 0.8403 (m) cc_final: 0.8111 (p) REVERT: C 76 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8427 (p0) REVERT: C 197 ARG cc_start: 0.8313 (mtp-110) cc_final: 0.7619 (mtm-85) REVERT: C 214 ARG cc_start: 0.8014 (mmt-90) cc_final: 0.7750 (mmm160) REVERT: C 215 GLU cc_start: 0.8250 (mp0) cc_final: 0.7605 (mp0) REVERT: D 20 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7806 (mtpm) REVERT: D 26 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: D 46 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8195 (mptt) REVERT: E 76 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7490 (pttt) REVERT: A 613 VAL cc_start: 0.7846 (p) cc_final: 0.7645 (t) REVERT: A 633 ARG cc_start: 0.6071 (OUTLIER) cc_final: 0.4713 (ttm170) REVERT: A 685 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7176 (tp) REVERT: A 758 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7790 (mm-30) outliers start: 44 outliers final: 28 residues processed: 156 average time/residue: 1.2237 time to fit residues: 205.1248 Evaluate side-chains 160 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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 21 LYS 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 173 ARG Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 214 TYR 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 189 SER 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 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 620 VAL Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 788 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 7 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116404 restraints weight = 9500.157| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.07 r_work: 0.3258 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8131 Z= 0.125 Angle : 0.517 8.710 11015 Z= 0.268 Chirality : 0.042 0.165 1240 Planarity : 0.004 0.041 1407 Dihedral : 4.879 50.700 1115 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.07 % Allowed : 26.64 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1001 helix: 2.64 (0.26), residues: 390 sheet: -0.50 (0.35), residues: 214 loop : -0.24 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 100 HIS 0.004 0.001 HIS B 213 PHE 0.011 0.001 PHE C 151 TYR 0.014 0.001 TYR E 80 ARG 0.006 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 416) hydrogen bonds : angle 4.04336 ( 1191) SS BOND : bond 0.00175 ( 2) SS BOND : angle 0.96893 ( 4) covalent geometry : bond 0.00291 ( 8129) covalent geometry : angle 0.51715 (11011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6650.75 seconds wall clock time: 116 minutes 10.58 seconds (6970.58 seconds total)