Starting phenix.real_space_refine on Mon May 12 01:41:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqe_60384/05_2025/8zqe_60384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqe_60384/05_2025/8zqe_60384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqe_60384/05_2025/8zqe_60384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqe_60384/05_2025/8zqe_60384.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqe_60384/05_2025/8zqe_60384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqe_60384/05_2025/8zqe_60384.cif" } resolution = 2.9 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= 0.002 sd= 0.032 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 64 5.16 5 C 5602 2.51 5 N 1490 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8767 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2192 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 1 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 2, 'TRANS': 7} Time building chain proxies: 4.92, per 1000 atoms: 0.56 Number of scatterers: 8767 At special positions: 0 Unit cell: (86.528, 117.312, 125.632, 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 64 16.00 O 1611 8.00 N 1490 7.00 C 5602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " 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: 2.13 Conformation dependent library (CDL) restraints added in 999.7 milliseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 37.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.576A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.590A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.724A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.844A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 61 through 65 removed outlier: 3.582A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.965A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.655A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 61 removed outlier: 3.633A pdb=" N ALA R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 85 removed outlier: 3.780A pdb=" N ILE R 70 " --> pdb=" O ARG R 66 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE R 71 " --> pdb=" O LEU R 67 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR R 85 " --> pdb=" O ILE R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.985A pdb=" N TRP R 89 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER R 95 " --> pdb=" O ASP R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.590A pdb=" N SER R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 172 Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 189 through 202 Processing helix chain 'R' and resid 204 through 229 removed outlier: 3.566A pdb=" N THR R 213 " --> pdb=" O LEU R 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER R 229 " --> pdb=" O HIS R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 270 removed outlier: 3.962A pdb=" N SER R 239 " --> pdb=" O LYS R 235 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 278 through 288 Processing helix chain 'R' and resid 289 through 291 No H-bonds generated for 'chain 'R' and resid 289 through 291' Processing helix chain 'R' and resid 292 through 305 removed outlier: 3.623A pdb=" N ASN R 298 " --> pdb=" O ASN R 294 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 307 through 315 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.849A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.229A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.719A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.621A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.621A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.545A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.639A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.716A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.418A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.754A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 135 removed outlier: 3.520A pdb=" N TYR S 215 " --> pdb=" O THR S 231 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 175 through 177 442 hydrogen bonds defined for protein. 1242 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: 2.36 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2213 1.33 - 1.45: 1854 1.45 - 1.58: 4797 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 8953 Sorted by residual: bond pdb=" N GLN B 175 " pdb=" CA GLN B 175 " ideal model delta sigma weight residual 1.458 1.492 -0.034 9.00e-03 1.23e+04 1.44e+01 bond pdb=" N VAL L 74 " pdb=" CA VAL L 74 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.10e-03 1.21e+04 1.34e+01 bond pdb=" N TRP R 89 " pdb=" CA TRP R 89 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.28e-02 6.10e+03 1.13e+01 bond pdb=" N VAL L 73 " pdb=" CA VAL L 73 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" N ILE A 344 " pdb=" CA ILE A 344 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.31e+00 ... (remaining 8948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 11617 1.61 - 3.22: 422 3.22 - 4.83: 72 4.83 - 6.44: 13 6.44 - 8.05: 6 Bond angle restraints: 12130 Sorted by residual: angle pdb=" C SER R 229 " pdb=" CA SER R 229 " pdb=" CB SER R 229 " ideal model delta sigma weight residual 116.63 110.91 5.72 1.16e+00 7.43e-01 2.43e+01 angle pdb=" N LEU R 36 " pdb=" CA LEU R 36 " pdb=" C LEU R 36 " ideal model delta sigma weight residual 113.25 107.44 5.81 1.30e+00 5.92e-01 1.99e+01 angle pdb=" N PHE R 82 " pdb=" CA PHE R 82 " pdb=" C PHE R 82 " ideal model delta sigma weight residual 111.36 106.96 4.40 1.09e+00 8.42e-01 1.63e+01 angle pdb=" N SER R 229 " pdb=" CA SER R 229 " pdb=" C SER R 229 " ideal model delta sigma weight residual 108.08 114.70 -6.62 1.69e+00 3.50e-01 1.53e+01 angle pdb=" N PHE A 334 " pdb=" CA PHE A 334 " pdb=" C PHE A 334 " ideal model delta sigma weight residual 111.07 107.04 4.03 1.07e+00 8.73e-01 1.42e+01 ... (remaining 12125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4822 17.86 - 35.72: 401 35.72 - 53.58: 62 53.58 - 71.44: 12 71.44 - 89.30: 8 Dihedral angle restraints: 5305 sinusoidal: 2029 harmonic: 3276 Sorted by residual: dihedral pdb=" CA GLU S 222 " pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta harmonic sigma weight residual -180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 58.75 34.25 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1094 0.054 - 0.107: 232 0.107 - 0.161: 48 0.161 - 0.214: 11 0.214 - 0.268: 1 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA ILE R 309 " pdb=" N ILE R 309 " pdb=" C ILE R 309 " pdb=" CB ILE R 309 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE R 279 " pdb=" N ILE R 279 " pdb=" C ILE R 279 " pdb=" CB ILE R 279 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA VAL B 307 " pdb=" N VAL B 307 " pdb=" C VAL B 307 " pdb=" CB VAL B 307 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 1383 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 306 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ASP R 306 " -0.060 2.00e-02 2.50e+03 pdb=" O ASP R 306 " 0.023 2.00e-02 2.50e+03 pdb=" N SER R 307 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 166 " 0.052 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO R 167 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO R 167 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 167 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 89 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C TRP R 89 " 0.036 2.00e-02 2.50e+03 pdb=" O TRP R 89 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL R 90 " -0.012 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 334 2.72 - 3.26: 9201 3.26 - 3.81: 14919 3.81 - 4.35: 18338 4.35 - 4.90: 31491 Nonbonded interactions: 74283 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.169 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU R 173 " pdb=" NZ LYS R 186 " model vdw 2.254 3.120 nonbonded pdb=" OG SER S 52 " pdb=" O SER S 55 " model vdw 2.266 3.040 ... (remaining 74278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.080 Find NCS groups from input model: 0.070 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:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.004 0.045 8956 Z= 0.274 Angle : 0.714 8.053 12136 Z= 0.453 Chirality : 0.049 0.268 1386 Planarity : 0.005 0.078 1524 Dihedral : 13.699 89.299 3180 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.21 % Allowed : 0.85 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1111 helix: 0.89 (0.26), residues: 391 sheet: -0.11 (0.33), residues: 270 loop : -0.89 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.007 0.001 HIS B 183 PHE 0.014 0.001 PHE A 334 TYR 0.020 0.002 TYR S 223 ARG 0.004 0.000 ARG S 190 Details of bonding type rmsd hydrogen bonds : bond 0.18796 ( 437) hydrogen bonds : angle 7.60646 ( 1242) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.89498 ( 6) covalent geometry : bond 0.00430 ( 8953) covalent geometry : angle 0.71414 (12130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 279 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7853 (mtmt) REVERT: A 243 MET cc_start: 0.7966 (tpp) cc_final: 0.7049 (tpp) REVERT: A 249 LEU cc_start: 0.8387 (tp) cc_final: 0.8088 (tp) REVERT: A 252 SER cc_start: 0.8467 (t) cc_final: 0.7858 (p) REVERT: A 315 ASP cc_start: 0.7213 (p0) cc_final: 0.6969 (p0) REVERT: B 8 ARG cc_start: 0.8210 (ptp90) cc_final: 0.7807 (ptp-110) REVERT: B 33 ILE cc_start: 0.8317 (pt) cc_final: 0.7994 (mt) REVERT: B 189 SER cc_start: 0.8297 (t) cc_final: 0.7991 (p) REVERT: B 210 LEU cc_start: 0.8122 (tp) cc_final: 0.7882 (tt) REVERT: B 260 GLU cc_start: 0.7136 (pt0) cc_final: 0.6907 (pt0) REVERT: B 261 LEU cc_start: 0.8129 (mt) cc_final: 0.7878 (mm) REVERT: B 262 MET cc_start: 0.7343 (mmt) cc_final: 0.7068 (mmm) REVERT: B 263 THR cc_start: 0.8074 (m) cc_final: 0.7777 (t) REVERT: C 20 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8081 (ttpt) REVERT: S 7 SER cc_start: 0.8340 (t) cc_final: 0.8096 (p) REVERT: S 63 THR cc_start: 0.7866 (t) cc_final: 0.7512 (m) REVERT: S 71 SER cc_start: 0.8281 (p) cc_final: 0.7903 (t) REVERT: S 90 ASP cc_start: 0.7981 (m-30) cc_final: 0.7648 (m-30) REVERT: S 116 THR cc_start: 0.8734 (t) cc_final: 0.8495 (m) REVERT: S 160 THR cc_start: 0.7899 (m) cc_final: 0.7630 (t) REVERT: S 218 MET cc_start: 0.7742 (ttp) cc_final: 0.7539 (ttp) REVERT: R 55 MET cc_start: 0.6273 (mtm) cc_final: 0.5883 (mtm) REVERT: R 124 LEU cc_start: 0.7036 (tp) cc_final: 0.6389 (mt) REVERT: R 200 LEU cc_start: 0.7357 (tp) cc_final: 0.7145 (tt) REVERT: R 300 PHE cc_start: 0.6486 (m-80) cc_final: 0.6240 (m-10) outliers start: 2 outliers final: 2 residues processed: 280 average time/residue: 0.9562 time to fit residues: 288.7102 Evaluate side-chains 236 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 110 ASN B 155 ASN B 176 GLN S 130 GLN S 167 GLN S 182 ASN R 233 ASN R 315 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.148708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125437 restraints weight = 13207.707| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.16 r_work: 0.3553 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8956 Z= 0.177 Angle : 0.645 8.806 12136 Z= 0.330 Chirality : 0.045 0.216 1386 Planarity : 0.005 0.064 1524 Dihedral : 4.648 21.823 1219 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.55 % Allowed : 13.53 % Favored : 81.92 % 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: 0.02 (0.26), residues: 1111 helix: 1.18 (0.26), residues: 393 sheet: -0.04 (0.32), residues: 277 loop : -0.96 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.019 0.002 PHE S 68 TYR 0.024 0.002 TYR S 59 ARG 0.007 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 437) hydrogen bonds : angle 5.19623 ( 1242) SS BOND : bond 0.00321 ( 3) SS BOND : angle 1.16910 ( 6) covalent geometry : bond 0.00392 ( 8953) covalent geometry : angle 0.64445 (12130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8231 (mttm) cc_final: 0.7986 (mtpp) REVERT: A 243 MET cc_start: 0.8559 (tpp) cc_final: 0.7878 (tpp) REVERT: A 249 LEU cc_start: 0.8540 (tp) cc_final: 0.8286 (tp) REVERT: A 252 SER cc_start: 0.8704 (t) cc_final: 0.8336 (p) REVERT: A 271 LYS cc_start: 0.8413 (pttt) cc_final: 0.7781 (pttm) REVERT: B 8 ARG cc_start: 0.8191 (ptp90) cc_final: 0.7931 (ptt-90) REVERT: B 17 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: B 19 ARG cc_start: 0.8024 (tmm160) cc_final: 0.7777 (ttp80) REVERT: B 33 ILE cc_start: 0.8468 (pt) cc_final: 0.8008 (mt) REVERT: B 96 ARG cc_start: 0.7759 (mpt90) cc_final: 0.7434 (mpt180) REVERT: B 214 ARG cc_start: 0.8662 (mmt90) cc_final: 0.8456 (mmt90) REVERT: B 221 THR cc_start: 0.8437 (t) cc_final: 0.8130 (m) REVERT: B 261 LEU cc_start: 0.8485 (mt) cc_final: 0.8270 (mm) REVERT: C 20 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8345 (ttpt) REVERT: C 21 MET cc_start: 0.7722 (ptm) cc_final: 0.7408 (ptm) REVERT: S 63 THR cc_start: 0.8265 (t) cc_final: 0.7977 (m) REVERT: S 79 LEU cc_start: 0.7967 (tm) cc_final: 0.7731 (tp) REVERT: S 93 MET cc_start: 0.8024 (ttt) cc_final: 0.7801 (ttp) REVERT: S 156 SER cc_start: 0.8347 (m) cc_final: 0.8129 (p) REVERT: S 161 TYR cc_start: 0.8516 (m-80) cc_final: 0.8264 (m-80) REVERT: S 201 THR cc_start: 0.8396 (p) cc_final: 0.8187 (t) REVERT: S 205 SER cc_start: 0.8511 (t) cc_final: 0.8165 (t) REVERT: R 55 MET cc_start: 0.7279 (mtm) cc_final: 0.6681 (mtm) REVERT: R 124 LEU cc_start: 0.7414 (tp) cc_final: 0.6770 (mt) REVERT: R 200 LEU cc_start: 0.7409 (tp) cc_final: 0.7171 (tt) REVERT: R 222 LEU cc_start: 0.7898 (mp) cc_final: 0.7505 (mt) REVERT: R 285 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5940 (pm20) REVERT: R 300 PHE cc_start: 0.7391 (m-80) cc_final: 0.7077 (m-10) outliers start: 43 outliers final: 11 residues processed: 285 average time/residue: 0.8654 time to fit residues: 267.4162 Evaluate side-chains 272 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 259 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 241 LYS Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 301 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 75 GLN B 183 HIS B 311 HIS S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.145334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122166 restraints weight = 13342.713| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.17 r_work: 0.3512 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8956 Z= 0.212 Angle : 0.640 8.692 12136 Z= 0.330 Chirality : 0.045 0.184 1386 Planarity : 0.005 0.058 1524 Dihedral : 4.575 23.623 1216 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.59 % Allowed : 17.86 % Favored : 78.54 % 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: 0.03 (0.26), residues: 1111 helix: 1.24 (0.26), residues: 393 sheet: -0.24 (0.32), residues: 283 loop : -0.84 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.020 0.002 PHE R 204 TYR 0.037 0.002 TYR S 59 ARG 0.011 0.001 ARG S 168 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 437) hydrogen bonds : angle 5.04815 ( 1242) SS BOND : bond 0.00427 ( 3) SS BOND : angle 1.00664 ( 6) covalent geometry : bond 0.00459 ( 8953) covalent geometry : angle 0.63963 (12130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8206 (pt0) cc_final: 0.7934 (pt0) REVERT: A 190 THR cc_start: 0.8515 (t) cc_final: 0.8289 (m) REVERT: A 197 LYS cc_start: 0.8234 (mttm) cc_final: 0.7681 (mtpp) REVERT: A 243 MET cc_start: 0.8649 (tpp) cc_final: 0.7950 (tpp) REVERT: A 249 LEU cc_start: 0.8508 (tp) cc_final: 0.8155 (tp) REVERT: A 252 SER cc_start: 0.8706 (t) cc_final: 0.8348 (p) REVERT: A 271 LYS cc_start: 0.8559 (pttt) cc_final: 0.7933 (pttm) REVERT: A 330 LYS cc_start: 0.8192 (mppt) cc_final: 0.7843 (mppt) REVERT: B 8 ARG cc_start: 0.8215 (ptp90) cc_final: 0.7916 (ptp-110) REVERT: B 17 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: B 22 ARG cc_start: 0.7361 (mtt180) cc_final: 0.7115 (mtt-85) REVERT: B 96 ARG cc_start: 0.7819 (mpt90) cc_final: 0.7537 (mpt180) REVERT: B 137 ARG cc_start: 0.7664 (mmm160) cc_final: 0.7274 (mmm160) REVERT: B 170 ASP cc_start: 0.7919 (m-30) cc_final: 0.7627 (t0) REVERT: B 214 ARG cc_start: 0.8644 (mmt90) cc_final: 0.8428 (mmt90) REVERT: B 221 THR cc_start: 0.8479 (t) cc_final: 0.8197 (m) REVERT: B 253 PHE cc_start: 0.8778 (m-80) cc_final: 0.8498 (m-80) REVERT: C 20 LYS cc_start: 0.8547 (ttpt) cc_final: 0.8267 (ttpt) REVERT: C 21 MET cc_start: 0.7842 (ptm) cc_final: 0.7549 (ptm) REVERT: S 58 ILE cc_start: 0.8753 (mm) cc_final: 0.8547 (OUTLIER) REVERT: S 63 THR cc_start: 0.8569 (t) cc_final: 0.8320 (m) REVERT: S 79 LEU cc_start: 0.8057 (tm) cc_final: 0.7835 (tp) REVERT: S 156 SER cc_start: 0.8454 (m) cc_final: 0.8216 (p) REVERT: S 205 SER cc_start: 0.8454 (t) cc_final: 0.8134 (t) REVERT: R 55 MET cc_start: 0.7387 (mtm) cc_final: 0.6732 (mtm) REVERT: R 71 PHE cc_start: 0.7693 (m-10) cc_final: 0.7114 (m-10) REVERT: R 117 MET cc_start: 0.7594 (tmm) cc_final: 0.7378 (tmm) REVERT: R 124 LEU cc_start: 0.7430 (tp) cc_final: 0.7103 (mt) REVERT: R 200 LEU cc_start: 0.7643 (tp) cc_final: 0.7431 (tt) REVERT: R 300 PHE cc_start: 0.7414 (m-80) cc_final: 0.7117 (m-10) REVERT: R 301 ILE cc_start: 0.8279 (mm) cc_final: 0.8053 (mp) outliers start: 34 outliers final: 21 residues processed: 275 average time/residue: 0.9706 time to fit residues: 287.2417 Evaluate side-chains 277 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 256 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 241 LYS Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.0570 chunk 69 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 176 GLN B 230 ASN S 130 GLN S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.147082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124281 restraints weight = 13268.554| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.18 r_work: 0.3549 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8956 Z= 0.116 Angle : 0.565 8.164 12136 Z= 0.288 Chirality : 0.042 0.217 1386 Planarity : 0.004 0.057 1524 Dihedral : 4.289 20.006 1216 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.38 % Allowed : 20.93 % Favored : 75.69 % 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: 0.08 (0.26), residues: 1111 helix: 1.38 (0.26), residues: 393 sheet: -0.21 (0.32), residues: 278 loop : -0.92 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.001 PHE R 204 TYR 0.028 0.002 TYR S 59 ARG 0.009 0.001 ARG S 168 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 437) hydrogen bonds : angle 4.74798 ( 1242) SS BOND : bond 0.00319 ( 3) SS BOND : angle 0.94831 ( 6) covalent geometry : bond 0.00249 ( 8953) covalent geometry : angle 0.56432 (12130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8246 (pt0) cc_final: 0.7953 (pt0) REVERT: A 190 THR cc_start: 0.8506 (t) cc_final: 0.8259 (m) REVERT: A 197 LYS cc_start: 0.8222 (mttm) cc_final: 0.7677 (mtpp) REVERT: A 243 MET cc_start: 0.8622 (tpp) cc_final: 0.7924 (tpp) REVERT: A 249 LEU cc_start: 0.8520 (tp) cc_final: 0.8196 (tp) REVERT: A 252 SER cc_start: 0.8692 (t) cc_final: 0.8366 (p) REVERT: A 271 LYS cc_start: 0.8507 (pttt) cc_final: 0.7861 (pttm) REVERT: A 275 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7866 (mm-30) REVERT: A 330 LYS cc_start: 0.8092 (mppt) cc_final: 0.7738 (mppt) REVERT: B 8 ARG cc_start: 0.8216 (ptp90) cc_final: 0.7931 (ptp-110) REVERT: B 50 THR cc_start: 0.8473 (m) cc_final: 0.8160 (t) REVERT: B 96 ARG cc_start: 0.7808 (mpt90) cc_final: 0.7563 (mpt180) REVERT: B 137 ARG cc_start: 0.7494 (mmm160) cc_final: 0.7210 (mmm160) REVERT: B 171 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7641 (mm) REVERT: B 214 ARG cc_start: 0.8656 (mmt90) cc_final: 0.8434 (mmt90) REVERT: B 221 THR cc_start: 0.8413 (t) cc_final: 0.8132 (m) REVERT: B 263 THR cc_start: 0.8543 (m) cc_final: 0.8295 (t) REVERT: C 20 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8252 (ttpt) REVERT: C 21 MET cc_start: 0.7760 (ptm) cc_final: 0.7468 (ptm) REVERT: S 18 ARG cc_start: 0.8163 (tpp-160) cc_final: 0.7722 (mmt-90) REVERT: S 63 THR cc_start: 0.8497 (t) cc_final: 0.8201 (m) REVERT: S 79 LEU cc_start: 0.8016 (tm) cc_final: 0.7799 (tp) REVERT: S 190 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7140 (ptt-90) REVERT: S 205 SER cc_start: 0.8412 (t) cc_final: 0.8080 (t) REVERT: R 55 MET cc_start: 0.7317 (mtm) cc_final: 0.6696 (mtm) REVERT: R 71 PHE cc_start: 0.7601 (m-10) cc_final: 0.7043 (m-10) REVERT: R 82 PHE cc_start: 0.7479 (t80) cc_final: 0.7069 (t80) REVERT: R 124 LEU cc_start: 0.7403 (tp) cc_final: 0.7196 (mt) REVERT: R 200 LEU cc_start: 0.7620 (tp) cc_final: 0.7369 (tt) REVERT: R 285 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6131 (pm20) REVERT: R 300 PHE cc_start: 0.7469 (m-80) cc_final: 0.7163 (m-10) REVERT: R 301 ILE cc_start: 0.8251 (mm) cc_final: 0.8026 (mp) outliers start: 32 outliers final: 16 residues processed: 280 average time/residue: 0.9798 time to fit residues: 295.0419 Evaluate side-chains 280 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 262 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 69 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 0.0470 chunk 41 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 176 GLN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.147546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124746 restraints weight = 13284.778| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.20 r_work: 0.3552 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8956 Z= 0.114 Angle : 0.554 9.222 12136 Z= 0.281 Chirality : 0.042 0.219 1386 Planarity : 0.004 0.056 1524 Dihedral : 4.167 20.100 1216 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.49 % Allowed : 21.56 % Favored : 74.95 % 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: 0.14 (0.26), residues: 1111 helix: 1.47 (0.26), residues: 393 sheet: -0.11 (0.32), residues: 269 loop : -0.96 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.001 PHE R 204 TYR 0.024 0.001 TYR S 59 ARG 0.009 0.000 ARG S 168 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 437) hydrogen bonds : angle 4.60506 ( 1242) SS BOND : bond 0.00308 ( 3) SS BOND : angle 0.86887 ( 6) covalent geometry : bond 0.00244 ( 8953) covalent geometry : angle 0.55362 (12130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8240 (pt0) cc_final: 0.7949 (pt0) REVERT: A 190 THR cc_start: 0.8524 (t) cc_final: 0.8262 (m) REVERT: A 197 LYS cc_start: 0.8229 (mttm) cc_final: 0.7705 (mtpp) REVERT: A 243 MET cc_start: 0.8676 (tpp) cc_final: 0.7953 (tpp) REVERT: A 249 LEU cc_start: 0.8515 (tp) cc_final: 0.8194 (tp) REVERT: A 252 SER cc_start: 0.8679 (t) cc_final: 0.8365 (p) REVERT: A 271 LYS cc_start: 0.8522 (pttt) cc_final: 0.8269 (pttp) REVERT: A 275 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7784 (mt-10) REVERT: A 330 LYS cc_start: 0.8083 (mppt) cc_final: 0.7712 (mppt) REVERT: B 8 ARG cc_start: 0.8263 (ptp90) cc_final: 0.7959 (ptp-110) REVERT: B 22 ARG cc_start: 0.7428 (mtt180) cc_final: 0.7222 (mtt180) REVERT: B 50 THR cc_start: 0.8500 (m) cc_final: 0.8203 (t) REVERT: B 96 ARG cc_start: 0.7853 (mpt90) cc_final: 0.7593 (mpt180) REVERT: B 214 ARG cc_start: 0.8697 (mmt90) cc_final: 0.8478 (mmt90) REVERT: B 221 THR cc_start: 0.8397 (t) cc_final: 0.8087 (m) REVERT: C 20 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8248 (ttpt) REVERT: C 21 MET cc_start: 0.7765 (ptm) cc_final: 0.7471 (ptm) REVERT: S 63 THR cc_start: 0.8482 (t) cc_final: 0.8224 (m) REVERT: S 79 LEU cc_start: 0.7953 (tm) cc_final: 0.7719 (tp) REVERT: S 161 TYR cc_start: 0.8352 (m-80) cc_final: 0.8135 (m-80) REVERT: S 205 SER cc_start: 0.8386 (t) cc_final: 0.8076 (t) REVERT: S 221 LEU cc_start: 0.8412 (tp) cc_final: 0.8203 (mm) REVERT: R 55 MET cc_start: 0.7329 (mtm) cc_final: 0.6703 (mtm) REVERT: R 71 PHE cc_start: 0.7611 (m-10) cc_final: 0.7031 (m-10) REVERT: R 81 ILE cc_start: 0.7211 (pt) cc_final: 0.6799 (pt) REVERT: R 82 PHE cc_start: 0.7568 (t80) cc_final: 0.7092 (t80) REVERT: R 112 MET cc_start: 0.5920 (mtp) cc_final: 0.5678 (ttp) REVERT: R 124 LEU cc_start: 0.7374 (tp) cc_final: 0.7006 (mt) REVERT: R 142 ARG cc_start: 0.6596 (ttm110) cc_final: 0.6299 (ttm110) REVERT: R 200 LEU cc_start: 0.7629 (tp) cc_final: 0.7356 (tt) REVERT: R 222 LEU cc_start: 0.7841 (mp) cc_final: 0.7534 (mt) REVERT: R 285 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6112 (pm20) REVERT: R 300 PHE cc_start: 0.7494 (m-80) cc_final: 0.7155 (m-10) REVERT: R 301 ILE cc_start: 0.8237 (mm) cc_final: 0.8019 (mp) outliers start: 33 outliers final: 16 residues processed: 271 average time/residue: 1.0197 time to fit residues: 296.7104 Evaluate side-chains 278 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 102 optimal weight: 0.0270 chunk 5 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.146204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123119 restraints weight = 13154.650| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.18 r_work: 0.3529 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8956 Z= 0.154 Angle : 0.581 8.917 12136 Z= 0.297 Chirality : 0.044 0.220 1386 Planarity : 0.004 0.055 1524 Dihedral : 4.259 19.406 1216 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.23 % Allowed : 21.88 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1111 helix: 1.49 (0.26), residues: 392 sheet: -0.33 (0.31), residues: 280 loop : -0.85 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.022 0.002 PHE S 68 TYR 0.038 0.002 TYR S 59 ARG 0.009 0.001 ARG S 168 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 437) hydrogen bonds : angle 4.65275 ( 1242) SS BOND : bond 0.00312 ( 3) SS BOND : angle 1.10344 ( 6) covalent geometry : bond 0.00335 ( 8953) covalent geometry : angle 0.58063 (12130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8235 (pt0) cc_final: 0.7932 (pt0) REVERT: A 190 THR cc_start: 0.8526 (t) cc_final: 0.8212 (m) REVERT: A 197 LYS cc_start: 0.8192 (mttm) cc_final: 0.7638 (mtpp) REVERT: A 243 MET cc_start: 0.8697 (tpp) cc_final: 0.8021 (tpp) REVERT: A 249 LEU cc_start: 0.8584 (tp) cc_final: 0.8269 (tp) REVERT: A 252 SER cc_start: 0.8703 (t) cc_final: 0.8390 (p) REVERT: A 271 LYS cc_start: 0.8578 (pttt) cc_final: 0.7931 (pttp) REVERT: A 275 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7718 (mt-10) REVERT: A 330 LYS cc_start: 0.8171 (mppt) cc_final: 0.7777 (mppt) REVERT: B 8 ARG cc_start: 0.8237 (ptp90) cc_final: 0.7944 (ptp-110) REVERT: B 50 THR cc_start: 0.8466 (m) cc_final: 0.8216 (t) REVERT: B 96 ARG cc_start: 0.7852 (mpt90) cc_final: 0.7601 (mpt180) REVERT: B 137 ARG cc_start: 0.7505 (mmm160) cc_final: 0.7249 (mmm160) REVERT: B 170 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: B 171 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7791 (mm) REVERT: B 214 ARG cc_start: 0.8689 (mmt90) cc_final: 0.8468 (mmt90) REVERT: B 221 THR cc_start: 0.8423 (t) cc_final: 0.8115 (m) REVERT: C 20 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8244 (ttpt) REVERT: C 21 MET cc_start: 0.7732 (ptm) cc_final: 0.7438 (ptm) REVERT: S 18 ARG cc_start: 0.8151 (tpp-160) cc_final: 0.7715 (mmt-90) REVERT: S 63 THR cc_start: 0.8422 (t) cc_final: 0.8142 (m) REVERT: S 79 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7767 (tp) REVERT: S 83 MET cc_start: 0.8233 (mtm) cc_final: 0.7794 (mtp) REVERT: S 205 SER cc_start: 0.8361 (t) cc_final: 0.8049 (t) REVERT: S 221 LEU cc_start: 0.8531 (tp) cc_final: 0.8315 (mm) REVERT: S 223 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.7303 (t80) REVERT: R 55 MET cc_start: 0.7301 (mtm) cc_final: 0.6685 (mtm) REVERT: R 71 PHE cc_start: 0.7730 (m-10) cc_final: 0.7108 (m-10) REVERT: R 81 ILE cc_start: 0.7416 (pt) cc_final: 0.7000 (pt) REVERT: R 82 PHE cc_start: 0.7698 (t80) cc_final: 0.7186 (t80) REVERT: R 112 MET cc_start: 0.5967 (mtp) cc_final: 0.5734 (ttp) REVERT: R 124 LEU cc_start: 0.7345 (tp) cc_final: 0.7011 (mt) REVERT: R 142 ARG cc_start: 0.6611 (ttm110) cc_final: 0.6310 (ttm110) REVERT: R 222 LEU cc_start: 0.7873 (mp) cc_final: 0.7591 (mt) REVERT: R 285 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6171 (pm20) REVERT: R 300 PHE cc_start: 0.7512 (m-80) cc_final: 0.7168 (m-10) REVERT: R 301 ILE cc_start: 0.8284 (mm) cc_final: 0.8077 (mp) outliers start: 40 outliers final: 21 residues processed: 283 average time/residue: 0.9722 time to fit residues: 296.0889 Evaluate side-chains 296 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 14 optimal weight: 0.0030 chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 32 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.146775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123778 restraints weight = 13367.395| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.20 r_work: 0.3537 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8956 Z= 0.133 Angle : 0.578 8.045 12136 Z= 0.295 Chirality : 0.043 0.195 1386 Planarity : 0.005 0.055 1524 Dihedral : 4.210 19.333 1216 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.02 % Allowed : 23.15 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1111 helix: 1.60 (0.26), residues: 391 sheet: -0.27 (0.31), residues: 280 loop : -0.87 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.026 0.002 PHE S 68 TYR 0.040 0.002 TYR S 59 ARG 0.012 0.001 ARG S 168 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 437) hydrogen bonds : angle 4.60026 ( 1242) SS BOND : bond 0.00297 ( 3) SS BOND : angle 0.85124 ( 6) covalent geometry : bond 0.00290 ( 8953) covalent geometry : angle 0.57833 (12130) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8230 (mmmt) cc_final: 0.7915 (ttmm) REVERT: A 33 GLU cc_start: 0.8240 (pt0) cc_final: 0.7939 (pt0) REVERT: A 197 LYS cc_start: 0.8210 (mttm) cc_final: 0.7669 (mtpp) REVERT: A 243 MET cc_start: 0.8701 (tpp) cc_final: 0.7986 (tpp) REVERT: A 271 LYS cc_start: 0.8592 (pttt) cc_final: 0.8328 (pttp) REVERT: A 275 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 330 LYS cc_start: 0.8156 (mppt) cc_final: 0.7757 (mppt) REVERT: B 8 ARG cc_start: 0.8247 (ptp90) cc_final: 0.7950 (ptp-110) REVERT: B 50 THR cc_start: 0.8447 (m) cc_final: 0.8182 (t) REVERT: B 96 ARG cc_start: 0.7844 (mpt90) cc_final: 0.7592 (mpt180) REVERT: B 119 ASN cc_start: 0.8094 (m-40) cc_final: 0.7815 (m-40) REVERT: B 137 ARG cc_start: 0.7497 (mmm160) cc_final: 0.7239 (mmm160) REVERT: B 170 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: B 171 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7749 (mm) REVERT: B 214 ARG cc_start: 0.8672 (mmt90) cc_final: 0.8459 (mmt90) REVERT: B 221 THR cc_start: 0.8384 (t) cc_final: 0.8111 (m) REVERT: C 20 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8232 (ttpt) REVERT: C 21 MET cc_start: 0.7709 (ptm) cc_final: 0.7411 (ptm) REVERT: S 63 THR cc_start: 0.8214 (t) cc_final: 0.7880 (m) REVERT: S 79 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7771 (tp) REVERT: S 205 SER cc_start: 0.8315 (t) cc_final: 0.8010 (t) REVERT: S 221 LEU cc_start: 0.8469 (tp) cc_final: 0.8264 (mm) REVERT: R 55 MET cc_start: 0.7311 (mtm) cc_final: 0.6706 (mtm) REVERT: R 71 PHE cc_start: 0.7760 (m-10) cc_final: 0.7131 (m-10) REVERT: R 81 ILE cc_start: 0.7411 (pt) cc_final: 0.7023 (pt) REVERT: R 82 PHE cc_start: 0.7713 (t80) cc_final: 0.7123 (t80) REVERT: R 112 MET cc_start: 0.5998 (mtp) cc_final: 0.5755 (ttp) REVERT: R 124 LEU cc_start: 0.7349 (tp) cc_final: 0.7004 (mt) REVERT: R 142 ARG cc_start: 0.6581 (ttm110) cc_final: 0.6279 (ttm110) REVERT: R 222 LEU cc_start: 0.7851 (mp) cc_final: 0.7553 (mt) REVERT: R 285 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6174 (pm20) REVERT: R 300 PHE cc_start: 0.7516 (m-80) cc_final: 0.7167 (m-10) outliers start: 38 outliers final: 21 residues processed: 283 average time/residue: 1.0402 time to fit residues: 317.5520 Evaluate side-chains 283 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN R 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.147524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124876 restraints weight = 13368.310| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.19 r_work: 0.3547 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8956 Z= 0.123 Angle : 0.588 8.407 12136 Z= 0.299 Chirality : 0.043 0.188 1386 Planarity : 0.004 0.058 1524 Dihedral : 4.189 19.332 1216 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.49 % Allowed : 25.48 % Favored : 71.04 % 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: 0.22 (0.26), residues: 1111 helix: 1.61 (0.26), residues: 394 sheet: -0.28 (0.31), residues: 279 loop : -0.85 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.026 0.001 PHE S 68 TYR 0.047 0.002 TYR S 59 ARG 0.008 0.001 ARG S 168 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 437) hydrogen bonds : angle 4.58743 ( 1242) SS BOND : bond 0.00401 ( 3) SS BOND : angle 0.89917 ( 6) covalent geometry : bond 0.00267 ( 8953) covalent geometry : angle 0.58737 (12130) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: A 17 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7912 (ttmm) REVERT: A 33 GLU cc_start: 0.8222 (pt0) cc_final: 0.7928 (pt0) REVERT: A 197 LYS cc_start: 0.8174 (mttm) cc_final: 0.7629 (mtpp) REVERT: A 243 MET cc_start: 0.8740 (tpp) cc_final: 0.8052 (tpp) REVERT: A 252 SER cc_start: 0.8626 (t) cc_final: 0.8354 (p) REVERT: A 271 LYS cc_start: 0.8595 (pttt) cc_final: 0.8332 (pttp) REVERT: A 275 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 330 LYS cc_start: 0.8125 (mppt) cc_final: 0.7724 (mppt) REVERT: B 8 ARG cc_start: 0.8249 (ptp90) cc_final: 0.7979 (ptp-110) REVERT: B 50 THR cc_start: 0.8419 (m) cc_final: 0.8142 (t) REVERT: B 96 ARG cc_start: 0.7877 (mpt90) cc_final: 0.7626 (mpt180) REVERT: B 137 ARG cc_start: 0.7450 (mmm160) cc_final: 0.7228 (mmm160) REVERT: B 170 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: B 171 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7697 (mm) REVERT: B 175 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6418 (mp10) REVERT: B 214 ARG cc_start: 0.8660 (mmt90) cc_final: 0.8451 (mmt90) REVERT: B 221 THR cc_start: 0.8342 (t) cc_final: 0.8064 (m) REVERT: C 20 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8233 (ttpt) REVERT: C 21 MET cc_start: 0.7727 (ptm) cc_final: 0.7435 (ptm) REVERT: S 63 THR cc_start: 0.7972 (t) cc_final: 0.7675 (m) REVERT: S 205 SER cc_start: 0.8270 (t) cc_final: 0.7966 (t) REVERT: R 55 MET cc_start: 0.7277 (mtm) cc_final: 0.6674 (mtm) REVERT: R 58 LEU cc_start: 0.8022 (mm) cc_final: 0.7498 (tt) REVERT: R 71 PHE cc_start: 0.7749 (m-10) cc_final: 0.7128 (m-10) REVERT: R 81 ILE cc_start: 0.7482 (pt) cc_final: 0.7123 (pt) REVERT: R 82 PHE cc_start: 0.7696 (t80) cc_final: 0.7317 (t80) REVERT: R 112 MET cc_start: 0.6037 (mtp) cc_final: 0.5818 (ttp) REVERT: R 285 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6245 (pm20) REVERT: R 300 PHE cc_start: 0.7503 (m-80) cc_final: 0.7151 (m-10) outliers start: 33 outliers final: 18 residues processed: 264 average time/residue: 0.9933 time to fit residues: 281.3114 Evaluate side-chains 279 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 256 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 chunk 101 optimal weight: 0.0870 chunk 99 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.148243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125212 restraints weight = 13401.648| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.22 r_work: 0.3555 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8956 Z= 0.117 Angle : 0.599 9.981 12136 Z= 0.300 Chirality : 0.043 0.215 1386 Planarity : 0.004 0.055 1524 Dihedral : 4.180 19.413 1216 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.07 % Allowed : 26.22 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.27 (0.26), residues: 1111 helix: 1.62 (0.26), residues: 394 sheet: -0.23 (0.32), residues: 278 loop : -0.82 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE R 204 TYR 0.047 0.001 TYR S 59 ARG 0.009 0.001 ARG S 168 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 437) hydrogen bonds : angle 4.59440 ( 1242) SS BOND : bond 0.00340 ( 3) SS BOND : angle 0.84920 ( 6) covalent geometry : bond 0.00253 ( 8953) covalent geometry : angle 0.59873 (12130) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 260 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: A 17 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7906 (ttmm) REVERT: A 33 GLU cc_start: 0.8183 (pt0) cc_final: 0.7892 (pt0) REVERT: A 197 LYS cc_start: 0.8176 (mttm) cc_final: 0.7631 (mtpp) REVERT: A 243 MET cc_start: 0.8748 (tpp) cc_final: 0.8047 (tpp) REVERT: A 252 SER cc_start: 0.8629 (t) cc_final: 0.8364 (p) REVERT: A 271 LYS cc_start: 0.8610 (pttt) cc_final: 0.8352 (pttp) REVERT: A 275 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 330 LYS cc_start: 0.8082 (mppt) cc_final: 0.7676 (mppt) REVERT: B 8 ARG cc_start: 0.8231 (ptp90) cc_final: 0.7921 (mtm110) REVERT: B 50 THR cc_start: 0.8400 (m) cc_final: 0.8121 (t) REVERT: B 96 ARG cc_start: 0.7868 (mpt90) cc_final: 0.7589 (mpt180) REVERT: B 171 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7783 (mm) REVERT: B 175 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6317 (mp10) REVERT: B 214 ARG cc_start: 0.8637 (mmt90) cc_final: 0.8430 (mmt90) REVERT: B 221 THR cc_start: 0.8333 (t) cc_final: 0.8058 (m) REVERT: B 315 VAL cc_start: 0.8259 (p) cc_final: 0.8037 (m) REVERT: C 20 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8236 (ttpt) REVERT: C 21 MET cc_start: 0.7717 (ptm) cc_final: 0.7428 (ptm) REVERT: S 205 SER cc_start: 0.8249 (t) cc_final: 0.7971 (t) REVERT: R 55 MET cc_start: 0.7304 (mtm) cc_final: 0.6710 (mtm) REVERT: R 58 LEU cc_start: 0.8013 (mm) cc_final: 0.7441 (tt) REVERT: R 71 PHE cc_start: 0.7746 (m-10) cc_final: 0.7143 (m-10) REVERT: R 81 ILE cc_start: 0.7436 (pt) cc_final: 0.7093 (pt) REVERT: R 82 PHE cc_start: 0.7696 (t80) cc_final: 0.7326 (t80) REVERT: R 112 MET cc_start: 0.6095 (mtp) cc_final: 0.5842 (ttp) REVERT: R 285 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6244 (pm20) REVERT: R 300 PHE cc_start: 0.7556 (m-80) cc_final: 0.7175 (m-10) outliers start: 29 outliers final: 16 residues processed: 266 average time/residue: 1.0045 time to fit residues: 286.9940 Evaluate side-chains 275 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 72 optimal weight: 0.0870 chunk 99 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.146858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.124633 restraints weight = 13375.114| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.19 r_work: 0.3549 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8956 Z= 0.128 Angle : 0.608 10.658 12136 Z= 0.305 Chirality : 0.043 0.220 1386 Planarity : 0.005 0.055 1524 Dihedral : 4.163 19.675 1216 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.43 % Allowed : 27.80 % Favored : 69.77 % 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: 0.29 (0.26), residues: 1111 helix: 1.62 (0.26), residues: 394 sheet: -0.25 (0.31), residues: 283 loop : -0.76 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE R 204 TYR 0.043 0.002 TYR S 59 ARG 0.009 0.001 ARG S 168 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 437) hydrogen bonds : angle 4.58985 ( 1242) SS BOND : bond 0.00321 ( 3) SS BOND : angle 0.91159 ( 6) covalent geometry : bond 0.00280 ( 8953) covalent geometry : angle 0.60807 (12130) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7963 (mp) cc_final: 0.7758 (mt) REVERT: A 8 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: A 17 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7928 (ttmm) REVERT: A 33 GLU cc_start: 0.8199 (pt0) cc_final: 0.7912 (pt0) REVERT: A 197 LYS cc_start: 0.8175 (mttm) cc_final: 0.7616 (mtpp) REVERT: A 243 MET cc_start: 0.8711 (tpp) cc_final: 0.8020 (tpp) REVERT: A 250 PHE cc_start: 0.8257 (t80) cc_final: 0.7944 (t80) REVERT: A 252 SER cc_start: 0.8620 (t) cc_final: 0.8328 (p) REVERT: A 271 LYS cc_start: 0.8617 (pttt) cc_final: 0.8351 (pttp) REVERT: A 275 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7768 (mt-10) REVERT: A 330 LYS cc_start: 0.8105 (mppt) cc_final: 0.7685 (mppt) REVERT: B 8 ARG cc_start: 0.8235 (ptp90) cc_final: 0.7931 (mtm110) REVERT: B 50 THR cc_start: 0.8396 (m) cc_final: 0.8145 (t) REVERT: B 96 ARG cc_start: 0.7835 (mpt90) cc_final: 0.7538 (mpt180) REVERT: B 137 ARG cc_start: 0.7468 (mmm160) cc_final: 0.7233 (mmm160) REVERT: B 155 ASN cc_start: 0.8265 (t0) cc_final: 0.7876 (t0) REVERT: B 171 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7700 (mm) REVERT: B 175 GLN cc_start: 0.6720 (OUTLIER) cc_final: 0.6361 (mp10) REVERT: B 214 ARG cc_start: 0.8627 (mmt90) cc_final: 0.8423 (mmt90) REVERT: B 221 THR cc_start: 0.8339 (t) cc_final: 0.8048 (m) REVERT: B 283 ARG cc_start: 0.8442 (tpt170) cc_final: 0.7997 (tpt90) REVERT: B 315 VAL cc_start: 0.8272 (p) cc_final: 0.7989 (m) REVERT: C 20 LYS cc_start: 0.8512 (ttpt) cc_final: 0.8236 (ttpt) REVERT: C 21 MET cc_start: 0.7765 (ptm) cc_final: 0.7472 (ptm) REVERT: S 57 THR cc_start: 0.7838 (m) cc_final: 0.7622 (m) REVERT: S 205 SER cc_start: 0.8244 (t) cc_final: 0.7974 (t) REVERT: R 58 LEU cc_start: 0.7943 (mm) cc_final: 0.7384 (tt) REVERT: R 71 PHE cc_start: 0.7765 (m-10) cc_final: 0.7171 (m-10) REVERT: R 81 ILE cc_start: 0.7572 (pt) cc_final: 0.7228 (pt) REVERT: R 82 PHE cc_start: 0.7781 (t80) cc_final: 0.7444 (t80) REVERT: R 112 MET cc_start: 0.6108 (mtp) cc_final: 0.5859 (ttp) REVERT: R 135 ILE cc_start: 0.8402 (mm) cc_final: 0.8189 (mt) REVERT: R 285 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6260 (pm20) REVERT: R 300 PHE cc_start: 0.7534 (m-80) cc_final: 0.7156 (m-10) outliers start: 23 outliers final: 12 residues processed: 266 average time/residue: 0.9812 time to fit residues: 280.5156 Evaluate side-chains 270 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 254 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.145153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.122428 restraints weight = 13394.875| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.20 r_work: 0.3512 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8956 Z= 0.163 Angle : 0.645 10.863 12136 Z= 0.324 Chirality : 0.044 0.199 1386 Planarity : 0.005 0.055 1524 Dihedral : 4.323 20.003 1216 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.22 % Allowed : 28.54 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1111 helix: 1.55 (0.26), residues: 393 sheet: -0.31 (0.31), residues: 285 loop : -0.78 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE R 204 TYR 0.043 0.002 TYR S 59 ARG 0.010 0.001 ARG S 168 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 437) hydrogen bonds : angle 4.70411 ( 1242) SS BOND : bond 0.00290 ( 3) SS BOND : angle 0.90979 ( 6) covalent geometry : bond 0.00362 ( 8953) covalent geometry : angle 0.64464 (12130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7941.02 seconds wall clock time: 137 minutes 10.25 seconds (8230.25 seconds total)