Starting phenix.real_space_refine on Sat Dec 28 20:09:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vv5_32138/12_2024/7vv5_32138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv5_32138/12_2024/7vv5_32138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vv5_32138/12_2024/7vv5_32138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv5_32138/12_2024/7vv5_32138.map" model { file = "/net/cci-nas-00/data/ceres_data/7vv5_32138/12_2024/7vv5_32138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv5_32138/12_2024/7vv5_32138.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 66 5.16 5 C 5660 2.51 5 N 1474 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8829 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 427 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1786 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2139 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 8, 'TRANS': 259} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.01, per 1000 atoms: 0.57 Number of scatterers: 8829 At special positions: 0 Unit cell: (116.772, 108.356, 104.148, 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 66 16.00 O 1629 8.00 N 1474 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " 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: 2.20 Conformation dependent library (CDL) restraints added in 1.2 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 37.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.671A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.505A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.492A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.819A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 4.123A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.338A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.640A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.730A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.529A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 94 removed outlier: 3.831A pdb=" N VAL R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.602A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 212 removed outlier: 3.926A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 236 Processing helix chain 'R' and resid 236 through 245 removed outlier: 4.339A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'R' and resid 286 through 288 No H-bonds generated for 'chain 'R' and resid 286 through 288' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.303A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.442A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.853A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.680A 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: 6.892A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.788A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.444A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.520A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.594A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.698A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.137A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.464A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1257 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: 2.43 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 2811 1.35 - 1.48: 2505 1.48 - 1.61: 3616 1.61 - 1.75: 2 1.75 - 1.88: 90 Bond restraints: 9024 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.669 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C ALA S 40 " pdb=" N PRO S 41 " ideal model delta sigma weight residual 1.333 1.415 -0.082 1.44e-02 4.82e+03 3.26e+01 bond pdb=" CG LEU B 79 " pdb=" CD2 LEU B 79 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.62e+00 bond pdb=" CG1 ILE B 123 " pdb=" CD1 ILE B 123 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.51e+00 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.99e+00 ... (remaining 9019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 11938 3.21 - 6.43: 258 6.43 - 9.64: 26 9.64 - 12.86: 3 12.86 - 16.07: 5 Bond angle restraints: 12230 Sorted by residual: angle pdb=" N PRO S 41 " pdb=" CA PRO S 41 " pdb=" C PRO S 41 " ideal model delta sigma weight residual 113.81 121.95 -8.14 1.45e+00 4.76e-01 3.15e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 130.63 -7.89 1.44e+00 4.82e-01 3.01e+01 angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 113.45 120.88 -7.43 1.39e+00 5.18e-01 2.85e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 131.52 -9.98 1.91e+00 2.74e-01 2.73e+01 angle pdb=" C TRP R 250 " pdb=" N LYS R 251 " pdb=" CA LYS R 251 " ideal model delta sigma weight residual 122.08 129.29 -7.21 1.47e+00 4.63e-01 2.41e+01 ... (remaining 12225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4521 17.14 - 34.27: 579 34.27 - 51.41: 199 51.41 - 68.55: 56 68.55 - 85.69: 12 Dihedral angle restraints: 5367 sinusoidal: 2131 harmonic: 3236 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.43 -66.43 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CA THR R 30 " pdb=" C THR R 30 " pdb=" N LEU R 31 " pdb=" CA LEU R 31 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP R 254 " pdb=" C ASP R 254 " pdb=" N VAL R 255 " pdb=" CA VAL R 255 " ideal model delta harmonic sigma weight residual -180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 5364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1130 0.082 - 0.164: 227 0.164 - 0.246: 20 0.246 - 0.329: 7 0.329 - 0.411: 1 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CB VAL A 218 " pdb=" CA VAL A 218 " pdb=" CG1 VAL A 218 " pdb=" CG2 VAL A 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1382 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER S 172 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO S 173 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO S 173 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 173 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.046 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO S 75 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL R 149 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.014 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1853 2.77 - 3.30: 7280 3.30 - 3.83: 15787 3.83 - 4.37: 18448 4.37 - 4.90: 32102 Nonbonded interactions: 75470 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.286 3.040 nonbonded pdb=" O GLY R 27 " pdb=" OH TYR R 89 " model vdw 2.291 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.297 3.040 nonbonded pdb=" O SER R 264 " pdb=" OG SER R 268 " model vdw 2.306 3.040 ... (remaining 75465 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: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.040 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.012 0.134 9024 Z= 0.753 Angle : 1.174 16.073 12230 Z= 0.632 Chirality : 0.067 0.411 1385 Planarity : 0.008 0.069 1530 Dihedral : 18.052 85.686 3269 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 10.86 % Allowed : 18.27 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.82 (0.21), residues: 1108 helix: -2.79 (0.16), residues: 387 sheet: -0.57 (0.29), residues: 279 loop : -1.65 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP S 47 HIS 0.011 0.003 HIS S 35 PHE 0.028 0.004 PHE B 151 TYR 0.023 0.004 TYR S 50 ARG 0.005 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 216 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8256 (m-30) cc_final: 0.8052 (m-30) REVERT: A 29 LYS cc_start: 0.7879 (tppt) cc_final: 0.7514 (tppt) REVERT: A 32 ARG cc_start: 0.8335 (ptp90) cc_final: 0.7888 (ptp-170) REVERT: A 205 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6655 (mtm180) REVERT: A 248 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8127 (mttp) REVERT: A 273 LEU cc_start: 0.8539 (tp) cc_final: 0.8186 (tp) REVERT: A 305 CYS cc_start: 0.8128 (t) cc_final: 0.7844 (p) REVERT: B 10 GLU cc_start: 0.8181 (tp30) cc_final: 0.7699 (tp30) REVERT: B 15 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8502 (mtmt) REVERT: B 127 LYS cc_start: 0.9073 (mptm) cc_final: 0.8839 (mmtp) REVERT: B 146 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8856 (tp) REVERT: B 172 GLU cc_start: 0.7580 (pp20) cc_final: 0.7307 (tm-30) REVERT: B 188 MET cc_start: 0.8860 (mmm) cc_final: 0.8497 (mmm) REVERT: S 23 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8647 (p) REVERT: R 22 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.5832 (tm) REVERT: R 24 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6586 (mm) REVERT: R 28 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7115 (mmpt) REVERT: R 32 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7658 (tp) REVERT: R 52 LEU cc_start: 0.9279 (mt) cc_final: 0.9052 (mt) REVERT: R 58 ARG cc_start: 0.7892 (mmt-90) cc_final: 0.7662 (mmp80) REVERT: R 152 LEU cc_start: 0.8596 (mt) cc_final: 0.8371 (mt) REVERT: R 278 ILE cc_start: 0.9025 (mt) cc_final: 0.8749 (mt) REVERT: R 289 TRP cc_start: 0.5361 (p-90) cc_final: 0.4344 (m-10) outliers start: 104 outliers final: 34 residues processed: 303 average time/residue: 1.1208 time to fit residues: 363.4413 Evaluate side-chains 223 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 204 GLN A 213 HIS A 255 ASN B 175 GLN B 259 GLN B 311 HIS S 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9024 Z= 0.195 Angle : 0.606 9.758 12230 Z= 0.311 Chirality : 0.043 0.213 1385 Planarity : 0.005 0.040 1530 Dihedral : 10.054 82.043 1368 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.11 % Allowed : 24.01 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.52 (0.24), residues: 1108 helix: 0.27 (0.25), residues: 381 sheet: 0.05 (0.31), residues: 262 loop : -1.01 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.020 0.001 PHE R 257 TYR 0.017 0.001 TYR R 222 ARG 0.007 0.001 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 1.134 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: B 10 GLU cc_start: 0.8215 (tp30) cc_final: 0.7861 (tp30) REVERT: B 23 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8532 (tmmm) REVERT: B 101 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8206 (mtm) REVERT: B 127 LYS cc_start: 0.9008 (mptm) cc_final: 0.8712 (mmtp) REVERT: B 146 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8796 (tp) REVERT: B 188 MET cc_start: 0.8803 (mmm) cc_final: 0.8497 (mmm) REVERT: G 20 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8734 (ttmm) REVERT: G 37 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8721 (mp) REVERT: S 62 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7466 (p0) REVERT: S 87 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7034 (mtp85) REVERT: R 22 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5443 (tm) REVERT: R 58 ARG cc_start: 0.7783 (mmt-90) cc_final: 0.7539 (mmp80) REVERT: R 221 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8068 (mp) REVERT: R 249 ILE cc_start: 0.8362 (mt) cc_final: 0.8149 (mm) REVERT: R 278 ILE cc_start: 0.8926 (mt) cc_final: 0.8640 (mt) outliers start: 49 outliers final: 16 residues processed: 232 average time/residue: 1.3771 time to fit residues: 338.2413 Evaluate side-chains 207 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 255 ASN B 36 ASN B 266 HIS G 24 ASN S 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9024 Z= 0.199 Angle : 0.589 10.304 12230 Z= 0.297 Chirality : 0.042 0.176 1385 Planarity : 0.004 0.033 1530 Dihedral : 8.536 81.630 1320 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.91 % Allowed : 26.20 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.18 (0.25), residues: 1108 helix: 1.24 (0.26), residues: 390 sheet: 0.06 (0.30), residues: 269 loop : -0.78 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.022 0.001 PHE R 257 TYR 0.019 0.001 TYR R 222 ARG 0.008 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8256 (tp30) cc_final: 0.7869 (tp30) REVERT: B 15 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8629 (mtmt) REVERT: B 23 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8502 (tmmm) REVERT: B 101 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8111 (mtm) REVERT: B 127 LYS cc_start: 0.8988 (mptm) cc_final: 0.8671 (mmtp) REVERT: B 146 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8839 (tp) REVERT: B 188 MET cc_start: 0.8832 (mmm) cc_final: 0.8502 (mmm) REVERT: B 197 ARG cc_start: 0.7512 (mmp-170) cc_final: 0.7286 (mmp-170) REVERT: B 226 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: G 17 GLU cc_start: 0.7819 (tp30) cc_final: 0.7140 (tp30) REVERT: G 20 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8679 (ttmm) REVERT: G 32 LYS cc_start: 0.8892 (tmtp) cc_final: 0.8567 (tptm) REVERT: G 37 LEU cc_start: 0.8992 (tp) cc_final: 0.8736 (mp) REVERT: S 87 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7081 (mtp85) REVERT: R 22 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5441 (tm) REVERT: R 58 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7394 (mmp80) REVERT: R 278 ILE cc_start: 0.8883 (mt) cc_final: 0.8565 (mt) outliers start: 47 outliers final: 20 residues processed: 223 average time/residue: 1.3337 time to fit residues: 315.2847 Evaluate side-chains 209 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 0.0030 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9024 Z= 0.216 Angle : 0.589 10.225 12230 Z= 0.297 Chirality : 0.042 0.157 1385 Planarity : 0.004 0.037 1530 Dihedral : 8.055 81.224 1314 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.11 % Allowed : 25.99 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.58 (0.25), residues: 1108 helix: 1.72 (0.27), residues: 383 sheet: 0.03 (0.30), residues: 277 loop : -0.49 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.015 0.001 PHE R 257 TYR 0.019 0.001 TYR R 222 ARG 0.009 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8228 (tm-30) REVERT: A 308 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7830 (mt-10) REVERT: B 10 GLU cc_start: 0.8275 (tp30) cc_final: 0.7940 (tp30) REVERT: B 15 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8563 (mtmt) REVERT: B 23 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8549 (tmmm) REVERT: B 101 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8121 (mtm) REVERT: B 127 LYS cc_start: 0.8993 (mptm) cc_final: 0.8687 (mmtp) REVERT: B 146 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8828 (tp) REVERT: B 188 MET cc_start: 0.8846 (mmm) cc_final: 0.8438 (mmm) REVERT: B 226 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: G 20 LYS cc_start: 0.8950 (ttmt) cc_final: 0.8679 (ttmm) REVERT: G 32 LYS cc_start: 0.8841 (tmtp) cc_final: 0.8588 (tmtp) REVERT: G 37 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8683 (mp) REVERT: S 87 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7161 (mtp85) REVERT: R 22 LEU cc_start: 0.5779 (OUTLIER) cc_final: 0.5446 (tm) REVERT: R 58 ARG cc_start: 0.7793 (mmt-90) cc_final: 0.7430 (mmp80) REVERT: R 208 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7634 (mmm160) REVERT: R 270 LEU cc_start: 0.8827 (tp) cc_final: 0.8526 (tm) REVERT: R 278 ILE cc_start: 0.8878 (mt) cc_final: 0.8551 (mt) outliers start: 49 outliers final: 25 residues processed: 222 average time/residue: 1.2984 time to fit residues: 305.8912 Evaluate side-chains 213 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9024 Z= 0.218 Angle : 0.589 10.038 12230 Z= 0.298 Chirality : 0.042 0.160 1385 Planarity : 0.004 0.034 1530 Dihedral : 7.865 80.815 1313 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.22 % Allowed : 26.83 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.75 (0.25), residues: 1108 helix: 1.89 (0.27), residues: 385 sheet: 0.12 (0.31), residues: 268 loop : -0.42 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.016 0.001 PHE R 183 TYR 0.018 0.001 TYR R 222 ARG 0.009 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 238 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6936 (tp30) REVERT: A 244 HIS cc_start: 0.8338 (m90) cc_final: 0.7855 (m90) REVERT: A 273 LEU cc_start: 0.8572 (tp) cc_final: 0.8264 (tp) REVERT: A 304 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8214 (tm-30) REVERT: A 308 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7750 (mt-10) REVERT: B 10 GLU cc_start: 0.8318 (tp30) cc_final: 0.7895 (tp30) REVERT: B 15 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8546 (mtmt) REVERT: B 101 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8111 (mtm) REVERT: B 127 LYS cc_start: 0.9021 (mptm) cc_final: 0.8716 (mmtp) REVERT: B 188 MET cc_start: 0.8829 (mmm) cc_final: 0.8409 (mmm) REVERT: B 226 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: G 17 GLU cc_start: 0.7620 (tp30) cc_final: 0.7418 (tp30) REVERT: G 20 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8696 (ttmm) REVERT: G 29 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8256 (mptp) REVERT: G 32 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8546 (tmtp) REVERT: G 37 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8686 (mp) REVERT: S 62 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7484 (p0) REVERT: S 87 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7191 (mtp85) REVERT: R 22 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5539 (tm) REVERT: R 58 ARG cc_start: 0.7769 (mmt-90) cc_final: 0.7440 (mmp80) REVERT: R 181 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7017 (tt0) REVERT: R 208 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7623 (mmm160) REVERT: R 270 LEU cc_start: 0.8816 (tp) cc_final: 0.8527 (tm) REVERT: R 278 ILE cc_start: 0.8865 (mt) cc_final: 0.8521 (mt) outliers start: 50 outliers final: 30 residues processed: 224 average time/residue: 1.3867 time to fit residues: 329.2464 Evaluate side-chains 224 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9024 Z= 0.184 Angle : 0.577 10.122 12230 Z= 0.292 Chirality : 0.042 0.162 1385 Planarity : 0.004 0.047 1530 Dihedral : 7.741 80.344 1313 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.22 % Allowed : 27.77 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.92 (0.26), residues: 1108 helix: 2.10 (0.27), residues: 385 sheet: 0.11 (0.30), residues: 268 loop : -0.31 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.012 0.001 PHE R 257 TYR 0.021 0.001 TYR R 222 ARG 0.010 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6955 (tp30) REVERT: A 244 HIS cc_start: 0.8333 (m90) cc_final: 0.7920 (m90) REVERT: A 304 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 308 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7761 (mt-10) REVERT: B 10 GLU cc_start: 0.8281 (tp30) cc_final: 0.7891 (tp30) REVERT: B 15 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8563 (mtmt) REVERT: B 46 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7326 (ttp80) REVERT: B 101 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8030 (mtm) REVERT: B 127 LYS cc_start: 0.8934 (mptm) cc_final: 0.8579 (mmtm) REVERT: B 146 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8797 (tm) REVERT: B 188 MET cc_start: 0.8816 (mmm) cc_final: 0.8386 (mmm) REVERT: B 226 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: G 20 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8706 (ttmm) REVERT: G 29 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8250 (mptp) REVERT: G 32 LYS cc_start: 0.8804 (tmtp) cc_final: 0.8560 (tmtp) REVERT: G 37 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8693 (mp) REVERT: S 62 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7494 (p0) REVERT: R 58 ARG cc_start: 0.7741 (mmt-90) cc_final: 0.7429 (mmp80) REVERT: R 181 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6985 (tt0) REVERT: R 270 LEU cc_start: 0.8804 (tp) cc_final: 0.8526 (tm) REVERT: R 278 ILE cc_start: 0.8839 (mt) cc_final: 0.8486 (mt) outliers start: 50 outliers final: 27 residues processed: 230 average time/residue: 1.3122 time to fit residues: 319.9631 Evaluate side-chains 221 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9024 Z= 0.208 Angle : 0.595 10.046 12230 Z= 0.298 Chirality : 0.042 0.165 1385 Planarity : 0.004 0.050 1530 Dihedral : 7.557 80.198 1309 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.70 % Allowed : 28.71 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1108 helix: 2.21 (0.27), residues: 385 sheet: 0.13 (0.31), residues: 268 loop : -0.26 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.028 0.001 PHE R 257 TYR 0.020 0.001 TYR R 222 ARG 0.011 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 GLU cc_start: 0.7246 (mm-30) cc_final: 0.7011 (tp30) REVERT: A 244 HIS cc_start: 0.8335 (m90) cc_final: 0.7937 (m90) REVERT: A 273 LEU cc_start: 0.8566 (tp) cc_final: 0.8275 (tp) REVERT: B 10 GLU cc_start: 0.8284 (tp30) cc_final: 0.7893 (tp30) REVERT: B 46 ARG cc_start: 0.7543 (mtm-85) cc_final: 0.7312 (ttp80) REVERT: B 101 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8033 (mtm) REVERT: B 127 LYS cc_start: 0.8963 (mptm) cc_final: 0.8620 (mmtm) REVERT: B 188 MET cc_start: 0.8824 (mmm) cc_final: 0.8382 (mmm) REVERT: B 226 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: G 20 LYS cc_start: 0.8985 (ttmt) cc_final: 0.8705 (ttmm) REVERT: G 29 LYS cc_start: 0.8490 (mmmt) cc_final: 0.8257 (mptp) REVERT: G 32 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8303 (tptm) REVERT: G 37 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8692 (mp) REVERT: S 43 LYS cc_start: 0.8303 (mppt) cc_final: 0.7989 (mttm) REVERT: S 62 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7501 (p0) REVERT: R 58 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.7473 (mmp80) REVERT: R 181 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: R 208 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7641 (mmm160) REVERT: R 270 LEU cc_start: 0.8786 (tp) cc_final: 0.8530 (tm) REVERT: R 278 ILE cc_start: 0.8831 (mt) cc_final: 0.8477 (mt) outliers start: 45 outliers final: 24 residues processed: 214 average time/residue: 1.3429 time to fit residues: 304.4325 Evaluate side-chains 213 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 77 ASN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9024 Z= 0.255 Angle : 0.615 10.352 12230 Z= 0.311 Chirality : 0.043 0.167 1385 Planarity : 0.004 0.052 1530 Dihedral : 7.543 79.838 1308 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.18 % Allowed : 29.02 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1108 helix: 2.17 (0.27), residues: 386 sheet: 0.21 (0.31), residues: 274 loop : -0.21 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS B 91 PHE 0.023 0.001 PHE R 257 TYR 0.021 0.002 TYR R 222 ARG 0.012 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 HIS cc_start: 0.8341 (m90) cc_final: 0.7969 (m90) REVERT: A 273 LEU cc_start: 0.8584 (tp) cc_final: 0.8276 (tp) REVERT: B 10 GLU cc_start: 0.8340 (tp30) cc_final: 0.7955 (tp30) REVERT: B 101 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8106 (mtm) REVERT: B 127 LYS cc_start: 0.9043 (mptm) cc_final: 0.8769 (mmtp) REVERT: B 130 GLU cc_start: 0.8141 (mp0) cc_final: 0.7917 (mp0) REVERT: B 188 MET cc_start: 0.8838 (mmm) cc_final: 0.8394 (mmm) REVERT: B 226 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: G 17 GLU cc_start: 0.7711 (tp30) cc_final: 0.7381 (tp30) REVERT: G 20 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8703 (ttmm) REVERT: G 29 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8234 (mptp) REVERT: G 32 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8440 (tmtp) REVERT: S 43 LYS cc_start: 0.8334 (mppt) cc_final: 0.8074 (mtmm) REVERT: S 62 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7478 (p0) REVERT: S 148 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7192 (mmm-85) REVERT: R 58 ARG cc_start: 0.7801 (mmt-90) cc_final: 0.7484 (mmp80) REVERT: R 181 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: R 208 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7587 (mmm160) REVERT: R 270 LEU cc_start: 0.8791 (tp) cc_final: 0.8539 (tm) REVERT: R 278 ILE cc_start: 0.8844 (mt) cc_final: 0.8490 (mt) outliers start: 40 outliers final: 27 residues processed: 207 average time/residue: 1.3512 time to fit residues: 296.2560 Evaluate side-chains 213 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 306 GLN B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9024 Z= 0.241 Angle : 0.626 10.277 12230 Z= 0.315 Chirality : 0.043 0.168 1385 Planarity : 0.004 0.053 1530 Dihedral : 7.453 79.236 1308 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.18 % Allowed : 29.33 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1108 helix: 2.19 (0.27), residues: 387 sheet: 0.19 (0.31), residues: 268 loop : -0.20 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.022 0.001 PHE R 257 TYR 0.020 0.002 TYR R 222 ARG 0.012 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 HIS cc_start: 0.8358 (m90) cc_final: 0.8003 (m90) REVERT: A 273 LEU cc_start: 0.8588 (tp) cc_final: 0.8268 (tp) REVERT: B 8 ARG cc_start: 0.7237 (mpt180) cc_final: 0.6921 (mtt90) REVERT: B 10 GLU cc_start: 0.8344 (tp30) cc_final: 0.7968 (tp30) REVERT: B 101 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8051 (mtm) REVERT: B 127 LYS cc_start: 0.9035 (mptm) cc_final: 0.8726 (mmtm) REVERT: B 130 GLU cc_start: 0.8121 (mp0) cc_final: 0.7885 (mp0) REVERT: B 188 MET cc_start: 0.8834 (mmm) cc_final: 0.8400 (mmm) REVERT: B 226 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: G 17 GLU cc_start: 0.7690 (tp30) cc_final: 0.7329 (tp30) REVERT: G 20 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8698 (ttmm) REVERT: G 29 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8225 (mptp) REVERT: G 32 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8390 (tmtp) REVERT: S 43 LYS cc_start: 0.8341 (mppt) cc_final: 0.8081 (mtmm) REVERT: S 62 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7465 (p0) REVERT: S 148 ARG cc_start: 0.7458 (mmm-85) cc_final: 0.7219 (mmm-85) REVERT: R 58 ARG cc_start: 0.7784 (mmt-90) cc_final: 0.7465 (mmp80) REVERT: R 181 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: R 208 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7570 (mmm160) REVERT: R 270 LEU cc_start: 0.8785 (tp) cc_final: 0.8535 (tm) REVERT: R 278 ILE cc_start: 0.8814 (mt) cc_final: 0.8465 (mt) outliers start: 40 outliers final: 28 residues processed: 205 average time/residue: 1.3868 time to fit residues: 300.9954 Evaluate side-chains 215 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 306 GLN B 36 ASN B 266 HIS G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9024 Z= 0.195 Angle : 0.601 9.640 12230 Z= 0.303 Chirality : 0.042 0.170 1385 Planarity : 0.004 0.053 1530 Dihedral : 7.272 78.949 1308 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.76 % Allowed : 30.06 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1108 helix: 2.22 (0.27), residues: 389 sheet: 0.21 (0.31), residues: 268 loop : -0.17 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.023 0.001 PHE R 257 TYR 0.019 0.001 TYR R 222 ARG 0.013 0.001 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 HIS cc_start: 0.8350 (m90) cc_final: 0.7984 (m90) REVERT: A 273 LEU cc_start: 0.8582 (tp) cc_final: 0.8256 (tp) REVERT: B 8 ARG cc_start: 0.7263 (mpt180) cc_final: 0.7041 (mtt90) REVERT: B 10 GLU cc_start: 0.8344 (tp30) cc_final: 0.7960 (tp30) REVERT: B 101 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7971 (mtm) REVERT: B 127 LYS cc_start: 0.9030 (mptm) cc_final: 0.8719 (mmtm) REVERT: B 130 GLU cc_start: 0.8121 (mp0) cc_final: 0.7864 (mp0) REVERT: B 146 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8815 (tm) REVERT: B 188 MET cc_start: 0.8804 (mmm) cc_final: 0.8363 (mmm) REVERT: B 226 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: G 17 GLU cc_start: 0.7709 (tp30) cc_final: 0.7370 (tp30) REVERT: G 20 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8752 (ttmm) REVERT: G 29 LYS cc_start: 0.8479 (mmmt) cc_final: 0.8213 (mptp) REVERT: G 32 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8451 (tmtp) REVERT: S 43 LYS cc_start: 0.8322 (mppt) cc_final: 0.8056 (mttm) REVERT: S 148 ARG cc_start: 0.7435 (mmm-85) cc_final: 0.7142 (mmm-85) REVERT: R 58 ARG cc_start: 0.7764 (mmt-90) cc_final: 0.7450 (mmp80) REVERT: R 208 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7568 (mmm160) REVERT: R 245 LEU cc_start: 0.8515 (tm) cc_final: 0.8294 (tm) REVERT: R 270 LEU cc_start: 0.8757 (tp) cc_final: 0.8515 (tm) REVERT: R 278 ILE cc_start: 0.8691 (mt) cc_final: 0.8361 (mt) outliers start: 36 outliers final: 23 residues processed: 203 average time/residue: 1.3271 time to fit residues: 286.3622 Evaluate side-chains 207 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 306 GLN B 36 ASN B 266 HIS G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.134326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.095913 restraints weight = 11828.628| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.20 r_work: 0.2996 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9024 Z= 0.171 Angle : 0.612 8.823 12230 Z= 0.306 Chirality : 0.042 0.171 1385 Planarity : 0.004 0.055 1530 Dihedral : 7.131 78.735 1308 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.92 % Allowed : 31.11 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1108 helix: 2.32 (0.27), residues: 383 sheet: 0.19 (0.31), residues: 268 loop : -0.17 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.023 0.001 PHE R 257 TYR 0.018 0.001 TYR R 222 ARG 0.013 0.001 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4783.94 seconds wall clock time: 86 minutes 19.53 seconds (5179.53 seconds total)