Starting phenix.real_space_refine on Sun Jun 8 00:41:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6u_25728/06_2025/7t6u_25728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6u_25728/06_2025/7t6u_25728.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/7t6u_25728/06_2025/7t6u_25728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6u_25728/06_2025/7t6u_25728.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6u_25728/06_2025/7t6u_25728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6u_25728/06_2025/7t6u_25728.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 5791 2.51 5 N 1516 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9033 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1763 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "R" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2346 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 285} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.10, per 1000 atoms: 0.68 Number of scatterers: 9033 At special positions: 0 Unit cell: (118.8, 115.56, 99.36, 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 1662 8.00 N 1516 7.00 C 5791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QXV L 21 " Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 38.9% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.948A pdb=" N ARG A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.514A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.595A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.163A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.721A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.687A pdb=" N LEU A 273 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 275 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.153A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.748A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.556A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.758A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.616A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.002A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 39 Proline residue: R 29 - end of helix Processing helix chain 'R' and resid 39 through 54 removed outlier: 3.757A pdb=" N VAL R 47 " --> pdb=" O GLY R 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY R 52 " --> pdb=" O ILE R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 76 removed outlier: 4.121A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 87 removed outlier: 3.613A pdb=" N VAL R 83 " --> pdb=" O PRO R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.652A pdb=" N HIS R 102 " --> pdb=" O CYS R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 137 removed outlier: 3.610A pdb=" N ALA R 133 " --> pdb=" O HIS R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 removed outlier: 3.815A pdb=" N LYS R 144 " --> pdb=" O SER R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 157 Processing helix chain 'R' and resid 157 through 163 Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'R' and resid 189 through 207 removed outlier: 3.824A pdb=" N VAL R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 removed outlier: 3.737A pdb=" N ILE R 219 " --> pdb=" O SER R 215 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA R 225 " --> pdb=" O TYR R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 253 removed outlier: 3.568A pdb=" N VAL R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 267 removed outlier: 3.730A pdb=" N VAL R 260 " --> pdb=" O PRO R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 275 Processing helix chain 'R' and resid 277 through 293 removed outlier: 4.066A pdb=" N ASP R 281 " --> pdb=" O TYR R 277 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.594A pdb=" N LEU R 290 " --> pdb=" O PRO R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 303 removed outlier: 3.566A pdb=" N LEU R 297 " --> pdb=" O PHE R 293 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 315 removed outlier: 3.545A pdb=" N HIS R 315 " --> pdb=" O GLU R 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.169A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.508A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.828A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.541A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.581A 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: 6.832A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.539A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.143A 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: 4.017A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.011A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.011A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.731A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 Processing sheet with id=AB5, first strand: chain 'R' and resid 164 through 168 removed outlier: 3.709A pdb=" N THR R 177 " --> pdb=" O THR R 165 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1218 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: 2.67 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1449 1.31 - 1.43: 2518 1.43 - 1.56: 5163 1.56 - 1.69: 1 1.69 - 1.81: 94 Bond restraints: 9225 Sorted by residual: bond pdb=" C QXV L 21 " pdb=" NXT QXV L 21 " ideal model delta sigma weight residual 1.339 1.445 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CA SER A 6 " pdb=" CB SER A 6 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.61e-02 3.86e+03 1.48e+01 bond pdb=" N TYR R 274 " pdb=" CA TYR R 274 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.06e-02 8.90e+03 1.19e+01 bond pdb=" N VAL R 160 " pdb=" CA VAL R 160 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N VAL R 284 " pdb=" CA VAL R 284 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 ... (remaining 9220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 11735 1.91 - 3.82: 619 3.82 - 5.73: 97 5.73 - 7.64: 29 7.64 - 9.55: 6 Bond angle restraints: 12486 Sorted by residual: angle pdb=" N PHE R 163 " pdb=" CA PHE R 163 " pdb=" C PHE R 163 " ideal model delta sigma weight residual 112.94 119.73 -6.79 1.41e+00 5.03e-01 2.32e+01 angle pdb=" N LEU R 263 " pdb=" CA LEU R 263 " pdb=" C LEU R 263 " ideal model delta sigma weight residual 111.82 106.40 5.42 1.16e+00 7.43e-01 2.18e+01 angle pdb=" C ASN R 285 " pdb=" CA ASN R 285 " pdb=" CB ASN R 285 " ideal model delta sigma weight residual 113.04 120.59 -7.55 1.63e+00 3.76e-01 2.15e+01 angle pdb=" N PRO R 286 " pdb=" CA PRO R 286 " pdb=" CB PRO R 286 " ideal model delta sigma weight residual 103.33 98.30 5.03 1.10e+00 8.26e-01 2.09e+01 angle pdb=" CA CYS R 176 " pdb=" C CYS R 176 " pdb=" O CYS R 176 " ideal model delta sigma weight residual 121.58 116.47 5.11 1.12e+00 7.97e-01 2.08e+01 ... (remaining 12481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 4947 16.90 - 33.80: 411 33.80 - 50.70: 76 50.70 - 67.60: 11 67.60 - 84.50: 5 Dihedral angle restraints: 5450 sinusoidal: 2131 harmonic: 3319 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -170.50 84.50 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CA GLU A 276 " pdb=" C GLU A 276 " pdb=" N LYS A 277 " pdb=" CA LYS A 277 " ideal model delta harmonic sigma weight residual -180.00 -148.96 -31.04 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" C ASN R 285 " pdb=" N ASN R 285 " pdb=" CA ASN R 285 " pdb=" CB ASN R 285 " ideal model delta harmonic sigma weight residual -122.60 -137.44 14.84 0 2.50e+00 1.60e-01 3.52e+01 ... (remaining 5447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1278 0.098 - 0.196: 127 0.196 - 0.293: 11 0.293 - 0.391: 4 0.391 - 0.489: 2 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA ASN R 285 " pdb=" N ASN R 285 " pdb=" C ASN R 285 " pdb=" CB ASN R 285 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA GLU R 270 " pdb=" N GLU R 270 " pdb=" C GLU R 270 " pdb=" CB GLU R 270 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CA ASN R 135 " pdb=" N ASN R 135 " pdb=" C ASN R 135 " pdb=" CB ASN R 135 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 1419 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO R 149 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 238 " 0.046 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO R 239 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO R 239 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 239 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 255 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO R 256 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO R 256 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 256 " -0.038 5.00e-02 4.00e+02 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2867 2.83 - 3.35: 7718 3.35 - 3.87: 15014 3.87 - 4.38: 17756 4.38 - 4.90: 30643 Nonbonded interactions: 73998 Sorted by model distance: nonbonded pdb=" OD2 ASP A 231 " pdb=" OG SER A 281 " model vdw 2.315 3.040 nonbonded pdb=" O ILE E 138 " pdb=" OG1 THR E 238 " model vdw 2.334 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.335 3.040 nonbonded pdb=" OG SER B 281 " pdb=" O HIS C 44 " model vdw 2.346 3.040 nonbonded pdb=" OE2 GLU A 28 " pdb=" OG SER R 140 " model vdw 2.347 3.040 ... (remaining 73993 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: 0.550 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.530 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 : 0.006 0.106 9228 Z= 0.323 Angle : 1.001 9.546 12492 Z= 0.635 Chirality : 0.064 0.489 1422 Planarity : 0.007 0.069 1565 Dihedral : 12.927 81.902 3301 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.31 % Allowed : 5.40 % Favored : 94.29 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.84 (0.20), residues: 1133 helix: -4.08 (0.14), residues: 399 sheet: -0.94 (0.28), residues: 284 loop : -1.88 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 132 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.002 PHE R 163 TYR 0.025 0.002 TYR R 175 ARG 0.006 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.27804 ( 427) hydrogen bonds : angle 10.34121 ( 1218) SS BOND : bond 0.00367 ( 3) SS BOND : angle 1.88065 ( 6) covalent geometry : bond 0.00574 ( 9225) covalent geometry : angle 0.99990 (12486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 248 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7859 (mtmm) REVERT: A 20 ASP cc_start: 0.7182 (p0) cc_final: 0.6953 (p0) REVERT: A 29 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7776 (mtpm) REVERT: A 186 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7005 (mt-10) REVERT: A 197 LYS cc_start: 0.7706 (mttt) cc_final: 0.7337 (mttm) REVERT: A 207 GLU cc_start: 0.7364 (tt0) cc_final: 0.7161 (tt0) REVERT: A 209 LYS cc_start: 0.7576 (ttpp) cc_final: 0.7252 (ttpp) REVERT: A 243 MET cc_start: 0.7534 (ttm) cc_final: 0.7160 (ttm) REVERT: A 245 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6981 (mm-30) REVERT: A 248 LYS cc_start: 0.7620 (ttmm) cc_final: 0.7347 (ttmm) REVERT: A 252 SER cc_start: 0.8215 (m) cc_final: 0.7938 (m) REVERT: A 271 LYS cc_start: 0.8393 (pttt) cc_final: 0.8105 (pttp) REVERT: A 294 ASN cc_start: 0.7803 (t0) cc_final: 0.7538 (t0) REVERT: A 309 ASP cc_start: 0.7273 (m-30) cc_final: 0.6922 (m-30) REVERT: A 318 GLU cc_start: 0.6838 (tp30) cc_final: 0.6612 (tp30) REVERT: B 147 SER cc_start: 0.8322 (m) cc_final: 0.8062 (p) REVERT: B 161 SER cc_start: 0.7917 (t) cc_final: 0.7698 (p) REVERT: B 163 ASP cc_start: 0.7317 (p0) cc_final: 0.6557 (p0) REVERT: B 186 ASP cc_start: 0.7521 (m-30) cc_final: 0.7281 (m-30) REVERT: B 217 MET cc_start: 0.6746 (mmm) cc_final: 0.6475 (mmm) REVERT: B 258 ASP cc_start: 0.7305 (t0) cc_final: 0.6696 (t0) REVERT: E 43 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8367 (ttmm) REVERT: E 84 THR cc_start: 0.8302 (m) cc_final: 0.7830 (p) REVERT: E 85 SER cc_start: 0.8373 (m) cc_final: 0.8019 (p) REVERT: E 155 VAL cc_start: 0.8654 (p) cc_final: 0.8301 (m) REVERT: E 186 GLN cc_start: 0.8114 (pt0) cc_final: 0.7801 (pt0) REVERT: E 210 THR cc_start: 0.7679 (p) cc_final: 0.7389 (m) REVERT: E 219 LEU cc_start: 0.8320 (tt) cc_final: 0.8118 (tm) REVERT: R 69 LEU cc_start: 0.8274 (mp) cc_final: 0.7859 (mp) REVERT: R 83 VAL cc_start: 0.7717 (p) cc_final: 0.7494 (m) REVERT: R 103 ILE cc_start: 0.8112 (mt) cc_final: 0.7902 (mm) REVERT: R 136 HIS cc_start: 0.7941 (m90) cc_final: 0.7728 (m-70) REVERT: R 214 MET cc_start: 0.7861 (tpp) cc_final: 0.7433 (tpp) REVERT: R 304 PHE cc_start: 0.7928 (m-10) cc_final: 0.7716 (m-80) outliers start: 3 outliers final: 1 residues processed: 251 average time/residue: 1.1599 time to fit residues: 311.2490 Evaluate side-chains 205 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 311 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 62 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 230 ASN B 237 ASN B 239 ASN B 259 GLN B 293 ASN E 194 ASN R 102 HIS R 108 ASN R 258 GLN R 307 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101087 restraints weight = 12421.719| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.72 r_work: 0.3202 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9228 Z= 0.155 Angle : 0.587 10.135 12492 Z= 0.313 Chirality : 0.043 0.139 1422 Planarity : 0.005 0.052 1565 Dihedral : 5.327 72.107 1266 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.47 % Allowed : 12.54 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.88 (0.22), residues: 1133 helix: -1.45 (0.22), residues: 402 sheet: -0.55 (0.28), residues: 293 loop : -1.32 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.004 0.001 HIS B 311 PHE 0.013 0.001 PHE B 235 TYR 0.014 0.001 TYR E 190 ARG 0.008 0.001 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 427) hydrogen bonds : angle 5.54823 ( 1218) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.71994 ( 6) covalent geometry : bond 0.00347 ( 9225) covalent geometry : angle 0.58686 (12486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8214 (mtm) REVERT: A 51 LYS cc_start: 0.8490 (mttm) cc_final: 0.8146 (mttm) REVERT: A 186 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7627 (mt-10) REVERT: A 197 LYS cc_start: 0.8343 (mttt) cc_final: 0.8014 (mttp) REVERT: A 209 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7878 (ttpp) REVERT: A 243 MET cc_start: 0.8039 (ttm) cc_final: 0.7659 (ttm) REVERT: A 245 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 271 LYS cc_start: 0.8742 (pttt) cc_final: 0.8404 (pttp) REVERT: A 283 LEU cc_start: 0.8654 (tp) cc_final: 0.8303 (tm) REVERT: A 294 ASN cc_start: 0.7900 (t0) cc_final: 0.7694 (t0) REVERT: A 309 ASP cc_start: 0.7777 (m-30) cc_final: 0.7454 (m-30) REVERT: A 318 GLU cc_start: 0.7493 (tp30) cc_final: 0.7288 (tp30) REVERT: B 38 ASP cc_start: 0.8407 (m-30) cc_final: 0.8093 (m-30) REVERT: B 147 SER cc_start: 0.8604 (m) cc_final: 0.8379 (p) REVERT: B 150 ARG cc_start: 0.8814 (mmt-90) cc_final: 0.8524 (mpt180) REVERT: B 163 ASP cc_start: 0.7599 (p0) cc_final: 0.7121 (p0) REVERT: B 217 MET cc_start: 0.7761 (mmm) cc_final: 0.7474 (mmm) REVERT: B 293 ASN cc_start: 0.8100 (m-40) cc_final: 0.7750 (m110) REVERT: B 312 ASP cc_start: 0.7913 (m-30) cc_final: 0.7563 (m-30) REVERT: B 338 ILE cc_start: 0.8648 (mm) cc_final: 0.8443 (mp) REVERT: E 43 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8436 (ttmm) REVERT: E 67 ARG cc_start: 0.8532 (mtm110) cc_final: 0.8305 (mtm-85) REVERT: E 68 PHE cc_start: 0.8289 (m-10) cc_final: 0.8018 (m-10) REVERT: E 84 THR cc_start: 0.8497 (m) cc_final: 0.8056 (p) REVERT: E 85 SER cc_start: 0.8670 (m) cc_final: 0.8462 (p) REVERT: E 155 VAL cc_start: 0.8619 (p) cc_final: 0.8404 (t) REVERT: E 186 GLN cc_start: 0.8462 (pt0) cc_final: 0.8222 (pt0) REVERT: E 210 THR cc_start: 0.7887 (p) cc_final: 0.7569 (m) REVERT: R 54 ARG cc_start: 0.7891 (mmm160) cc_final: 0.7656 (mtp85) REVERT: R 69 LEU cc_start: 0.8464 (mp) cc_final: 0.8231 (mp) REVERT: R 137 ARG cc_start: 0.8499 (ttt-90) cc_final: 0.7995 (ttt90) REVERT: R 211 SER cc_start: 0.8294 (t) cc_final: 0.8076 (p) REVERT: R 288 SER cc_start: 0.8270 (p) cc_final: 0.8005 (m) outliers start: 34 outliers final: 17 residues processed: 244 average time/residue: 1.3716 time to fit residues: 357.2275 Evaluate side-chains 227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 237 ASN B 239 ASN B 268 ASN R 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.100130 restraints weight = 12580.151| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.72 r_work: 0.3194 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9228 Z= 0.149 Angle : 0.551 8.624 12492 Z= 0.287 Chirality : 0.043 0.136 1422 Planarity : 0.004 0.048 1565 Dihedral : 4.976 65.364 1265 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.87 % Allowed : 15.80 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.24), residues: 1133 helix: -0.18 (0.25), residues: 415 sheet: -0.34 (0.28), residues: 290 loop : -1.04 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE B 235 TYR 0.013 0.001 TYR E 190 ARG 0.006 0.001 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 427) hydrogen bonds : angle 5.03367 ( 1218) SS BOND : bond 0.00313 ( 3) SS BOND : angle 0.67033 ( 6) covalent geometry : bond 0.00343 ( 9225) covalent geometry : angle 0.55096 (12486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8220 (mtm) REVERT: A 32 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.7920 (ttm-80) REVERT: A 186 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7609 (mt-10) REVERT: A 197 LYS cc_start: 0.8333 (mttt) cc_final: 0.8020 (mttp) REVERT: A 209 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7851 (ttpp) REVERT: A 243 MET cc_start: 0.8035 (ttm) cc_final: 0.7799 (ttm) REVERT: A 245 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7504 (mm-30) REVERT: A 271 LYS cc_start: 0.8779 (pttt) cc_final: 0.8460 (pttp) REVERT: A 283 LEU cc_start: 0.8641 (tp) cc_final: 0.8297 (tm) REVERT: A 294 ASN cc_start: 0.7909 (t0) cc_final: 0.7701 (t0) REVERT: A 309 ASP cc_start: 0.7733 (m-30) cc_final: 0.7329 (m-30) REVERT: A 318 GLU cc_start: 0.7539 (tp30) cc_final: 0.7327 (tp30) REVERT: B 45 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8345 (mtm) REVERT: B 132 ASN cc_start: 0.8243 (p0) cc_final: 0.8035 (p0) REVERT: B 134 ARG cc_start: 0.8457 (mtm110) cc_final: 0.8218 (ttp80) REVERT: B 147 SER cc_start: 0.8554 (m) cc_final: 0.8237 (p) REVERT: B 150 ARG cc_start: 0.8827 (mmt-90) cc_final: 0.8526 (mpt180) REVERT: B 163 ASP cc_start: 0.7541 (p0) cc_final: 0.7053 (p0) REVERT: B 217 MET cc_start: 0.7809 (mmm) cc_final: 0.7516 (mmm) REVERT: B 312 ASP cc_start: 0.7937 (m-30) cc_final: 0.7603 (m-30) REVERT: E 43 LYS cc_start: 0.8676 (mmmm) cc_final: 0.8410 (ttmm) REVERT: E 67 ARG cc_start: 0.8602 (mtm110) cc_final: 0.8374 (mtp180) REVERT: E 68 PHE cc_start: 0.8265 (m-10) cc_final: 0.7883 (m-10) REVERT: E 84 THR cc_start: 0.8498 (m) cc_final: 0.8037 (p) REVERT: E 85 SER cc_start: 0.8682 (m) cc_final: 0.8467 (p) REVERT: E 155 VAL cc_start: 0.8596 (p) cc_final: 0.8396 (t) REVERT: E 186 GLN cc_start: 0.8478 (pt0) cc_final: 0.8165 (pt0) REVERT: E 202 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8089 (mtm-85) REVERT: E 210 THR cc_start: 0.7876 (p) cc_final: 0.7587 (m) REVERT: R 54 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7559 (mtp85) REVERT: R 69 LEU cc_start: 0.8447 (mp) cc_final: 0.8187 (mp) REVERT: R 137 ARG cc_start: 0.8567 (ttt-90) cc_final: 0.8124 (ttt90) REVERT: R 201 ARG cc_start: 0.8148 (ttt90) cc_final: 0.7729 (ttt-90) REVERT: R 266 VAL cc_start: 0.8233 (t) cc_final: 0.7880 (m) REVERT: R 284 VAL cc_start: 0.7946 (p) cc_final: 0.7686 (t) REVERT: R 288 SER cc_start: 0.8355 (p) cc_final: 0.8091 (m) outliers start: 38 outliers final: 18 residues processed: 231 average time/residue: 1.3368 time to fit residues: 328.3639 Evaluate side-chains 225 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 65 optimal weight: 0.0470 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 155 ASN B 237 ASN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.111839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098440 restraints weight = 12432.917| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.71 r_work: 0.3168 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9228 Z= 0.247 Angle : 0.594 8.314 12492 Z= 0.310 Chirality : 0.046 0.148 1422 Planarity : 0.004 0.045 1565 Dihedral : 5.101 62.457 1265 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.28 % Allowed : 16.72 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1133 helix: 0.16 (0.25), residues: 415 sheet: -0.22 (0.29), residues: 290 loop : -1.03 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.010 0.001 HIS B 142 PHE 0.020 0.002 PHE R 163 TYR 0.014 0.002 TYR E 190 ARG 0.004 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 427) hydrogen bonds : angle 5.01106 ( 1218) SS BOND : bond 0.00346 ( 3) SS BOND : angle 0.83147 ( 6) covalent geometry : bond 0.00580 ( 9225) covalent geometry : angle 0.59360 (12486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8242 (mtm) REVERT: A 186 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 197 LYS cc_start: 0.8349 (mttt) cc_final: 0.8038 (mttp) REVERT: A 209 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7869 (ttpp) REVERT: A 243 MET cc_start: 0.8109 (ttm) cc_final: 0.7687 (ttm) REVERT: A 245 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7519 (mm-30) REVERT: A 271 LYS cc_start: 0.8791 (pttt) cc_final: 0.8466 (pttp) REVERT: A 283 LEU cc_start: 0.8618 (tp) cc_final: 0.8288 (tm) REVERT: A 294 ASN cc_start: 0.7985 (t0) cc_final: 0.7759 (t0) REVERT: A 309 ASP cc_start: 0.7731 (m-30) cc_final: 0.7309 (m-30) REVERT: A 318 GLU cc_start: 0.7515 (tp30) cc_final: 0.7313 (tp30) REVERT: A 329 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7889 (m) REVERT: A 337 ASP cc_start: 0.8059 (m-30) cc_final: 0.7837 (m-30) REVERT: A 341 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8274 (m-30) REVERT: B 132 ASN cc_start: 0.8350 (p0) cc_final: 0.8130 (p0) REVERT: B 142 HIS cc_start: 0.8514 (OUTLIER) cc_final: 0.8029 (t-90) REVERT: B 163 ASP cc_start: 0.7633 (p0) cc_final: 0.7255 (p0) REVERT: B 197 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7883 (mtp85) REVERT: B 217 MET cc_start: 0.7758 (mmm) cc_final: 0.7512 (mmm) REVERT: B 258 ASP cc_start: 0.7939 (t0) cc_final: 0.7354 (t0) REVERT: B 312 ASP cc_start: 0.7947 (m-30) cc_final: 0.7606 (m-30) REVERT: C 21 MET cc_start: 0.8216 (mtm) cc_final: 0.7978 (mtm) REVERT: E 43 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8409 (ttmm) REVERT: E 85 SER cc_start: 0.8697 (m) cc_final: 0.8454 (p) REVERT: E 91 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8288 (p) REVERT: E 115 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8229 (p) REVERT: E 155 VAL cc_start: 0.8598 (p) cc_final: 0.8393 (t) REVERT: E 186 GLN cc_start: 0.8476 (pt0) cc_final: 0.8234 (pt0) REVERT: E 202 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8007 (mtm-85) REVERT: E 210 THR cc_start: 0.7961 (p) cc_final: 0.7644 (m) REVERT: R 54 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7672 (mtp85) REVERT: R 69 LEU cc_start: 0.8490 (mp) cc_final: 0.8277 (mp) REVERT: R 137 ARG cc_start: 0.8611 (ttt-90) cc_final: 0.8156 (ttt90) REVERT: R 161 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6822 (t80) REVERT: R 201 ARG cc_start: 0.8165 (ttt90) cc_final: 0.7747 (ttt-90) REVERT: R 266 VAL cc_start: 0.8258 (t) cc_final: 0.7891 (m) REVERT: R 284 VAL cc_start: 0.8058 (p) cc_final: 0.7814 (t) REVERT: R 288 SER cc_start: 0.8336 (p) cc_final: 0.8049 (m) REVERT: R 310 ARG cc_start: 0.7929 (mtm110) cc_final: 0.7672 (mtp180) outliers start: 42 outliers final: 24 residues processed: 231 average time/residue: 1.6177 time to fit residues: 397.4137 Evaluate side-chains 245 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 237 ASN B 268 ASN E 39 GLN E 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103117 restraints weight = 12477.623| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.78 r_work: 0.3186 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9228 Z= 0.118 Angle : 0.524 9.569 12492 Z= 0.273 Chirality : 0.042 0.140 1422 Planarity : 0.004 0.044 1565 Dihedral : 4.771 60.885 1265 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.87 % Allowed : 18.04 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1133 helix: 0.69 (0.27), residues: 415 sheet: -0.23 (0.30), residues: 281 loop : -0.86 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.002 0.001 HIS B 311 PHE 0.023 0.001 PHE E 68 TYR 0.015 0.001 TYR E 190 ARG 0.007 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 427) hydrogen bonds : angle 4.76944 ( 1218) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.57225 ( 6) covalent geometry : bond 0.00265 ( 9225) covalent geometry : angle 0.52438 (12486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 1.756 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8237 (mtm) REVERT: A 32 ARG cc_start: 0.8258 (mtm-85) cc_final: 0.7950 (ttm-80) REVERT: A 186 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7601 (mt-10) REVERT: A 197 LYS cc_start: 0.8366 (mttt) cc_final: 0.8059 (mttp) REVERT: A 209 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7792 (ttpp) REVERT: A 210 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8197 (mmtt) REVERT: A 245 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7478 (mm-30) REVERT: A 271 LYS cc_start: 0.8787 (pttt) cc_final: 0.8489 (pttp) REVERT: A 283 LEU cc_start: 0.8610 (tp) cc_final: 0.8279 (tm) REVERT: A 294 ASN cc_start: 0.7942 (t0) cc_final: 0.7706 (t0) REVERT: A 309 ASP cc_start: 0.7745 (m-30) cc_final: 0.7324 (m-30) REVERT: A 318 GLU cc_start: 0.7525 (tp30) cc_final: 0.7320 (tp30) REVERT: A 329 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7778 (m) REVERT: A 337 ASP cc_start: 0.8061 (m-30) cc_final: 0.7839 (m-30) REVERT: B 132 ASN cc_start: 0.8267 (p0) cc_final: 0.8035 (p0) REVERT: B 147 SER cc_start: 0.8441 (m) cc_final: 0.8216 (p) REVERT: B 150 ARG cc_start: 0.8811 (mmt-90) cc_final: 0.8495 (mpt180) REVERT: B 163 ASP cc_start: 0.7595 (p0) cc_final: 0.7114 (p0) REVERT: B 217 MET cc_start: 0.7775 (mmm) cc_final: 0.7511 (mmm) REVERT: B 312 ASP cc_start: 0.7959 (m-30) cc_final: 0.7631 (m-30) REVERT: C 21 MET cc_start: 0.8214 (mtm) cc_final: 0.7952 (mtm) REVERT: E 68 PHE cc_start: 0.8204 (m-10) cc_final: 0.7919 (m-10) REVERT: E 84 THR cc_start: 0.8493 (m) cc_final: 0.8060 (p) REVERT: E 85 SER cc_start: 0.8778 (m) cc_final: 0.8434 (p) REVERT: E 115 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8176 (p) REVERT: E 186 GLN cc_start: 0.8456 (pt0) cc_final: 0.8144 (pt0) REVERT: E 202 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.7925 (mtm-85) REVERT: E 210 THR cc_start: 0.7944 (p) cc_final: 0.7664 (m) REVERT: E 218 ARG cc_start: 0.7803 (ptp-110) cc_final: 0.7576 (ptp-110) REVERT: R 69 LEU cc_start: 0.8449 (mp) cc_final: 0.8193 (mp) REVERT: R 137 ARG cc_start: 0.8584 (ttt-90) cc_final: 0.8195 (ttt90) REVERT: R 168 THR cc_start: 0.8010 (m) cc_final: 0.7803 (t) REVERT: R 250 PHE cc_start: 0.8291 (t80) cc_final: 0.7743 (t80) REVERT: R 266 VAL cc_start: 0.8223 (t) cc_final: 0.7874 (m) REVERT: R 283 LEU cc_start: 0.8119 (mt) cc_final: 0.7870 (mt) REVERT: R 284 VAL cc_start: 0.8022 (p) cc_final: 0.7771 (t) REVERT: R 310 ARG cc_start: 0.7873 (mtm110) cc_final: 0.7672 (mtp180) outliers start: 38 outliers final: 20 residues processed: 236 average time/residue: 1.6410 time to fit residues: 414.6787 Evaluate side-chains 235 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 155 ASN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102199 restraints weight = 12401.465| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.76 r_work: 0.3189 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9228 Z= 0.145 Angle : 0.538 9.214 12492 Z= 0.279 Chirality : 0.043 0.135 1422 Planarity : 0.004 0.043 1565 Dihedral : 4.756 60.872 1265 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.77 % Allowed : 18.96 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.09 (0.25), residues: 1133 helix: 0.85 (0.27), residues: 415 sheet: -0.13 (0.30), residues: 290 loop : -0.78 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS B 311 PHE 0.021 0.001 PHE E 68 TYR 0.014 0.001 TYR E 190 ARG 0.006 0.000 ARG R 54 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 427) hydrogen bonds : angle 4.74748 ( 1218) SS BOND : bond 0.00303 ( 3) SS BOND : angle 0.58694 ( 6) covalent geometry : bond 0.00335 ( 9225) covalent geometry : angle 0.53767 (12486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.7960 (ttm-80) REVERT: A 186 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7590 (mt-10) REVERT: A 197 LYS cc_start: 0.8361 (mttt) cc_final: 0.8022 (mttp) REVERT: A 209 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7792 (ttpp) REVERT: A 210 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8237 (mmtt) REVERT: A 245 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 251 ASP cc_start: 0.7537 (p0) cc_final: 0.7333 (t0) REVERT: A 271 LYS cc_start: 0.8801 (pttt) cc_final: 0.8486 (pttp) REVERT: A 283 LEU cc_start: 0.8611 (tp) cc_final: 0.8289 (tm) REVERT: A 309 ASP cc_start: 0.7738 (m-30) cc_final: 0.7316 (m-30) REVERT: A 318 GLU cc_start: 0.7506 (tp30) cc_final: 0.7305 (tp30) REVERT: A 329 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7809 (m) REVERT: B 49 ARG cc_start: 0.8720 (mmt90) cc_final: 0.8385 (tpp-160) REVERT: B 132 ASN cc_start: 0.8277 (p0) cc_final: 0.8041 (p0) REVERT: B 163 ASP cc_start: 0.7564 (p0) cc_final: 0.7142 (p0) REVERT: B 217 MET cc_start: 0.7751 (mmm) cc_final: 0.7507 (mmm) REVERT: B 312 ASP cc_start: 0.7978 (m-30) cc_final: 0.7659 (m-30) REVERT: C 21 MET cc_start: 0.8159 (mtm) cc_final: 0.7902 (mtm) REVERT: E 84 THR cc_start: 0.8473 (m) cc_final: 0.8033 (p) REVERT: E 85 SER cc_start: 0.8781 (m) cc_final: 0.8432 (p) REVERT: E 186 GLN cc_start: 0.8464 (pt0) cc_final: 0.8220 (pt0) REVERT: E 202 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.8093 (mtm-85) REVERT: E 210 THR cc_start: 0.8000 (p) cc_final: 0.7705 (m) REVERT: R 56 THR cc_start: 0.8680 (t) cc_final: 0.8379 (p) REVERT: R 69 LEU cc_start: 0.8432 (mp) cc_final: 0.8153 (mp) REVERT: R 137 ARG cc_start: 0.8605 (ttt-90) cc_final: 0.8191 (ttt90) REVERT: R 250 PHE cc_start: 0.8290 (t80) cc_final: 0.7713 (t80) REVERT: R 266 VAL cc_start: 0.8210 (t) cc_final: 0.7889 (m) REVERT: R 283 LEU cc_start: 0.8127 (mt) cc_final: 0.7857 (mt) REVERT: R 284 VAL cc_start: 0.7997 (p) cc_final: 0.7767 (t) REVERT: R 304 PHE cc_start: 0.8141 (m-10) cc_final: 0.7892 (m-80) REVERT: R 310 ARG cc_start: 0.7902 (mtm110) cc_final: 0.7447 (mtm110) outliers start: 37 outliers final: 24 residues processed: 237 average time/residue: 1.5033 time to fit residues: 379.7006 Evaluate side-chains 236 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 142 HIS B 155 ASN B 220 GLN B 237 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102532 restraints weight = 12564.905| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.77 r_work: 0.3188 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9228 Z= 0.145 Angle : 0.539 9.598 12492 Z= 0.280 Chirality : 0.043 0.134 1422 Planarity : 0.004 0.042 1565 Dihedral : 4.750 60.631 1265 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.16 % Allowed : 20.59 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1133 helix: 0.96 (0.27), residues: 415 sheet: -0.15 (0.30), residues: 286 loop : -0.69 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.009 0.001 HIS B 225 PHE 0.029 0.001 PHE E 68 TYR 0.014 0.001 TYR E 190 ARG 0.005 0.000 ARG R 54 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 427) hydrogen bonds : angle 4.71519 ( 1218) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.60069 ( 6) covalent geometry : bond 0.00337 ( 9225) covalent geometry : angle 0.53877 (12486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7955 (ttm-80) REVERT: A 186 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 197 LYS cc_start: 0.8362 (mttt) cc_final: 0.8023 (mttp) REVERT: A 209 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7802 (ttpp) REVERT: A 210 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8251 (mmtt) REVERT: A 245 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 251 ASP cc_start: 0.7557 (p0) cc_final: 0.7337 (t0) REVERT: A 271 LYS cc_start: 0.8805 (pttt) cc_final: 0.8484 (pttp) REVERT: A 283 LEU cc_start: 0.8607 (tp) cc_final: 0.8309 (tm) REVERT: A 294 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7680 (t0) REVERT: A 309 ASP cc_start: 0.7757 (m-30) cc_final: 0.7312 (m-30) REVERT: A 317 LYS cc_start: 0.8392 (ptpp) cc_final: 0.8187 (ptmt) REVERT: A 318 GLU cc_start: 0.7514 (tp30) cc_final: 0.7305 (tp30) REVERT: A 329 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7835 (m) REVERT: B 49 ARG cc_start: 0.8706 (mmt90) cc_final: 0.8397 (tpp-160) REVERT: B 132 ASN cc_start: 0.8288 (p0) cc_final: 0.8051 (p0) REVERT: B 142 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.8201 (t-170) REVERT: B 150 ARG cc_start: 0.8810 (mmt-90) cc_final: 0.8481 (mpt180) REVERT: B 163 ASP cc_start: 0.7610 (p0) cc_final: 0.7207 (p0) REVERT: B 217 MET cc_start: 0.7792 (mmm) cc_final: 0.7548 (mmm) REVERT: B 312 ASP cc_start: 0.7990 (m-30) cc_final: 0.7673 (m-30) REVERT: C 21 MET cc_start: 0.8147 (mtm) cc_final: 0.7904 (mtm) REVERT: E 84 THR cc_start: 0.8479 (m) cc_final: 0.8069 (p) REVERT: E 85 SER cc_start: 0.8807 (m) cc_final: 0.8450 (p) REVERT: E 186 GLN cc_start: 0.8468 (pt0) cc_final: 0.8144 (pt0) REVERT: E 202 ARG cc_start: 0.8310 (mtm-85) cc_final: 0.8092 (mtm-85) REVERT: E 210 THR cc_start: 0.7988 (p) cc_final: 0.7702 (m) REVERT: R 56 THR cc_start: 0.8667 (t) cc_final: 0.8370 (p) REVERT: R 69 LEU cc_start: 0.8440 (mp) cc_final: 0.8189 (mp) REVERT: R 137 ARG cc_start: 0.8630 (ttt-90) cc_final: 0.8227 (ttt90) REVERT: R 250 PHE cc_start: 0.8271 (t80) cc_final: 0.7721 (t80) REVERT: R 266 VAL cc_start: 0.8214 (t) cc_final: 0.7892 (m) REVERT: R 283 LEU cc_start: 0.8140 (mt) cc_final: 0.7865 (mt) REVERT: R 284 VAL cc_start: 0.7993 (p) cc_final: 0.7758 (t) REVERT: R 304 PHE cc_start: 0.7982 (m-10) cc_final: 0.7690 (m-80) REVERT: R 310 ARG cc_start: 0.7915 (mtm110) cc_final: 0.7555 (mtm110) outliers start: 31 outliers final: 20 residues processed: 230 average time/residue: 1.3288 time to fit residues: 323.8516 Evaluate side-chains 234 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 142 HIS B 155 ASN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102189 restraints weight = 12701.484| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.78 r_work: 0.3174 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9228 Z= 0.150 Angle : 0.548 9.729 12492 Z= 0.283 Chirality : 0.043 0.132 1422 Planarity : 0.004 0.042 1565 Dihedral : 4.761 60.593 1265 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.98 % Allowed : 20.08 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.09 (0.25), residues: 1133 helix: 1.10 (0.27), residues: 409 sheet: -0.09 (0.30), residues: 285 loop : -0.73 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.007 0.001 HIS B 225 PHE 0.022 0.001 PHE R 163 TYR 0.013 0.001 TYR B 111 ARG 0.005 0.000 ARG R 54 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 427) hydrogen bonds : angle 4.70841 ( 1218) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.64305 ( 6) covalent geometry : bond 0.00350 ( 9225) covalent geometry : angle 0.54789 (12486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7956 (ttm-80) REVERT: A 186 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7618 (mt-10) REVERT: A 197 LYS cc_start: 0.8379 (mttt) cc_final: 0.8041 (mttp) REVERT: A 209 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7801 (ttpp) REVERT: A 210 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8258 (mmtt) REVERT: A 245 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 251 ASP cc_start: 0.7528 (p0) cc_final: 0.7320 (t0) REVERT: A 271 LYS cc_start: 0.8787 (pttt) cc_final: 0.8474 (pttp) REVERT: A 283 LEU cc_start: 0.8591 (tp) cc_final: 0.8298 (tm) REVERT: A 309 ASP cc_start: 0.7754 (m-30) cc_final: 0.7309 (m-30) REVERT: A 317 LYS cc_start: 0.8400 (ptpp) cc_final: 0.8196 (ptmt) REVERT: A 318 GLU cc_start: 0.7518 (tp30) cc_final: 0.7307 (tp30) REVERT: B 49 ARG cc_start: 0.8705 (mmt90) cc_final: 0.8392 (tpp-160) REVERT: B 132 ASN cc_start: 0.8286 (p0) cc_final: 0.8046 (p0) REVERT: B 142 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.8048 (t-170) REVERT: B 150 ARG cc_start: 0.8813 (mmt-90) cc_final: 0.8486 (mpt180) REVERT: B 163 ASP cc_start: 0.7674 (p0) cc_final: 0.7251 (p0) REVERT: B 217 MET cc_start: 0.7768 (mmm) cc_final: 0.7524 (mmm) REVERT: B 312 ASP cc_start: 0.7983 (m-30) cc_final: 0.7669 (m-30) REVERT: C 21 MET cc_start: 0.8158 (mtm) cc_final: 0.7927 (mtm) REVERT: E 68 PHE cc_start: 0.7940 (m-10) cc_final: 0.7350 (m-10) REVERT: E 84 THR cc_start: 0.8477 (m) cc_final: 0.8021 (p) REVERT: E 85 SER cc_start: 0.8770 (m) cc_final: 0.8377 (p) REVERT: E 186 GLN cc_start: 0.8466 (pt0) cc_final: 0.8136 (pt0) REVERT: E 210 THR cc_start: 0.8041 (p) cc_final: 0.7754 (m) REVERT: R 41 VAL cc_start: 0.8447 (t) cc_final: 0.8111 (p) REVERT: R 56 THR cc_start: 0.8652 (t) cc_final: 0.8354 (p) REVERT: R 69 LEU cc_start: 0.8438 (mp) cc_final: 0.8184 (mp) REVERT: R 137 ARG cc_start: 0.8632 (ttt-90) cc_final: 0.8228 (ttt90) REVERT: R 250 PHE cc_start: 0.8273 (t80) cc_final: 0.7734 (t80) REVERT: R 266 VAL cc_start: 0.8217 (t) cc_final: 0.7897 (m) REVERT: R 283 LEU cc_start: 0.8121 (mt) cc_final: 0.7843 (mt) REVERT: R 284 VAL cc_start: 0.7988 (p) cc_final: 0.7749 (t) REVERT: R 304 PHE cc_start: 0.7987 (m-10) cc_final: 0.7786 (m-80) REVERT: R 310 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7537 (mtm110) outliers start: 39 outliers final: 28 residues processed: 231 average time/residue: 1.2654 time to fit residues: 312.0337 Evaluate side-chains 234 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 155 ASN B 237 ASN B 268 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101859 restraints weight = 12590.034| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.76 r_work: 0.3186 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9228 Z= 0.151 Angle : 0.557 10.467 12492 Z= 0.288 Chirality : 0.043 0.133 1422 Planarity : 0.004 0.042 1565 Dihedral : 4.737 60.541 1265 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.87 % Allowed : 20.80 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.16 (0.25), residues: 1133 helix: 1.19 (0.27), residues: 405 sheet: -0.05 (0.30), residues: 285 loop : -0.71 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.006 0.001 HIS B 225 PHE 0.017 0.001 PHE R 93 TYR 0.015 0.001 TYR B 111 ARG 0.006 0.000 ARG R 54 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 427) hydrogen bonds : angle 4.70222 ( 1218) SS BOND : bond 0.00269 ( 3) SS BOND : angle 0.62278 ( 6) covalent geometry : bond 0.00354 ( 9225) covalent geometry : angle 0.55655 (12486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7956 (ttm-80) REVERT: A 186 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 197 LYS cc_start: 0.8384 (mttt) cc_final: 0.8042 (mttp) REVERT: A 209 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7797 (ttpp) REVERT: A 210 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8258 (mmtt) REVERT: A 232 LEU cc_start: 0.8666 (mm) cc_final: 0.8307 (mp) REVERT: A 245 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7537 (mm-30) REVERT: A 251 ASP cc_start: 0.7511 (p0) cc_final: 0.7228 (t0) REVERT: A 271 LYS cc_start: 0.8788 (pttt) cc_final: 0.8474 (pttp) REVERT: A 283 LEU cc_start: 0.8591 (tp) cc_final: 0.8302 (tm) REVERT: A 309 ASP cc_start: 0.7757 (m-30) cc_final: 0.7306 (m-30) REVERT: A 318 GLU cc_start: 0.7533 (tp30) cc_final: 0.7322 (tp30) REVERT: B 49 ARG cc_start: 0.8669 (mmt90) cc_final: 0.8420 (tpp-160) REVERT: B 132 ASN cc_start: 0.8266 (p0) cc_final: 0.8034 (p0) REVERT: B 150 ARG cc_start: 0.8845 (mmt-90) cc_final: 0.8508 (mpt180) REVERT: B 163 ASP cc_start: 0.7666 (p0) cc_final: 0.7257 (p0) REVERT: B 217 MET cc_start: 0.7761 (mmm) cc_final: 0.7526 (mmm) REVERT: B 312 ASP cc_start: 0.7999 (m-30) cc_final: 0.7691 (m-30) REVERT: C 21 MET cc_start: 0.8151 (mtm) cc_final: 0.7930 (mtm) REVERT: E 84 THR cc_start: 0.8482 (m) cc_final: 0.8024 (p) REVERT: E 85 SER cc_start: 0.8751 (m) cc_final: 0.8373 (p) REVERT: E 141 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8544 (p) REVERT: E 186 GLN cc_start: 0.8471 (pt0) cc_final: 0.8144 (pt0) REVERT: E 210 THR cc_start: 0.8039 (p) cc_final: 0.7769 (m) REVERT: R 56 THR cc_start: 0.8660 (t) cc_final: 0.8362 (p) REVERT: R 69 LEU cc_start: 0.8439 (mp) cc_final: 0.8167 (mp) REVERT: R 137 ARG cc_start: 0.8652 (ttt-90) cc_final: 0.8240 (ttt90) REVERT: R 233 MET cc_start: 0.8500 (mtt) cc_final: 0.8275 (mtt) REVERT: R 250 PHE cc_start: 0.8269 (t80) cc_final: 0.7712 (t80) REVERT: R 266 VAL cc_start: 0.8223 (t) cc_final: 0.7900 (m) REVERT: R 283 LEU cc_start: 0.8129 (mt) cc_final: 0.7840 (mt) REVERT: R 284 VAL cc_start: 0.7998 (p) cc_final: 0.7761 (t) REVERT: R 304 PHE cc_start: 0.8011 (m-10) cc_final: 0.7681 (m-80) REVERT: R 310 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7566 (mtm-85) outliers start: 38 outliers final: 28 residues processed: 232 average time/residue: 1.1866 time to fit residues: 293.5891 Evaluate side-chains 237 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 46 optimal weight: 0.0670 chunk 66 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 155 ASN B 237 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101896 restraints weight = 12706.095| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.85 r_work: 0.3184 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9228 Z= 0.108 Angle : 0.539 11.858 12492 Z= 0.276 Chirality : 0.042 0.134 1422 Planarity : 0.004 0.043 1565 Dihedral : 4.543 60.057 1265 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.26 % Allowed : 21.10 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.28 (0.25), residues: 1133 helix: 1.36 (0.27), residues: 406 sheet: -0.04 (0.30), residues: 276 loop : -0.68 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.022 0.001 PHE R 163 TYR 0.014 0.001 TYR B 111 ARG 0.007 0.000 ARG R 54 Details of bonding type rmsd hydrogen bonds : bond 0.03197 ( 427) hydrogen bonds : angle 4.59214 ( 1218) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.43416 ( 6) covalent geometry : bond 0.00245 ( 9225) covalent geometry : angle 0.53902 (12486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 197 LYS cc_start: 0.8362 (mttt) cc_final: 0.7994 (mttp) REVERT: A 209 LYS cc_start: 0.7964 (ttpp) cc_final: 0.7730 (ttpp) REVERT: A 210 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8175 (mmtt) REVERT: A 232 LEU cc_start: 0.8613 (mm) cc_final: 0.8287 (mp) REVERT: A 245 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 251 ASP cc_start: 0.7518 (p0) cc_final: 0.7203 (t0) REVERT: A 271 LYS cc_start: 0.8760 (pttt) cc_final: 0.8424 (pttp) REVERT: A 283 LEU cc_start: 0.8578 (tp) cc_final: 0.8264 (tm) REVERT: A 309 ASP cc_start: 0.7666 (m-30) cc_final: 0.7193 (m-30) REVERT: A 317 LYS cc_start: 0.8253 (ptmt) cc_final: 0.7895 (ptpt) REVERT: A 318 GLU cc_start: 0.7583 (tp30) cc_final: 0.7342 (tp30) REVERT: A 329 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7879 (m) REVERT: B 38 ASP cc_start: 0.8380 (m-30) cc_final: 0.8146 (m-30) REVERT: B 114 CYS cc_start: 0.7904 (p) cc_final: 0.7698 (p) REVERT: B 132 ASN cc_start: 0.8219 (p0) cc_final: 0.7966 (p0) REVERT: B 150 ARG cc_start: 0.8815 (mmt-90) cc_final: 0.8467 (mpt180) REVERT: B 155 ASN cc_start: 0.8066 (t0) cc_final: 0.7637 (t0) REVERT: B 312 ASP cc_start: 0.7983 (m-30) cc_final: 0.7669 (m-30) REVERT: C 21 MET cc_start: 0.8121 (mtm) cc_final: 0.7889 (mtm) REVERT: E 68 PHE cc_start: 0.7729 (m-10) cc_final: 0.7371 (m-10) REVERT: E 84 THR cc_start: 0.8470 (m) cc_final: 0.8006 (p) REVERT: E 85 SER cc_start: 0.8725 (m) cc_final: 0.8324 (p) REVERT: E 119 VAL cc_start: 0.8255 (t) cc_final: 0.8037 (m) REVERT: E 141 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8554 (p) REVERT: E 186 GLN cc_start: 0.8457 (pt0) cc_final: 0.8133 (pt0) REVERT: E 210 THR cc_start: 0.8032 (p) cc_final: 0.7765 (m) REVERT: R 26 ARG cc_start: 0.8264 (ttm110) cc_final: 0.7904 (ttp80) REVERT: R 56 THR cc_start: 0.8620 (t) cc_final: 0.8317 (p) REVERT: R 58 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7829 (p) REVERT: R 137 ARG cc_start: 0.8640 (ttt-90) cc_final: 0.8243 (ttt90) REVERT: R 201 ARG cc_start: 0.8049 (ttt90) cc_final: 0.7573 (ttt-90) REVERT: R 233 MET cc_start: 0.8497 (mtt) cc_final: 0.8263 (mtt) REVERT: R 250 PHE cc_start: 0.8149 (t80) cc_final: 0.7664 (t80) REVERT: R 266 VAL cc_start: 0.8210 (t) cc_final: 0.7862 (m) REVERT: R 283 LEU cc_start: 0.8062 (mt) cc_final: 0.7760 (mt) REVERT: R 284 VAL cc_start: 0.7915 (p) cc_final: 0.7670 (t) REVERT: R 304 PHE cc_start: 0.7946 (m-10) cc_final: 0.7654 (m-80) REVERT: R 310 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7623 (mtm110) outliers start: 32 outliers final: 22 residues processed: 226 average time/residue: 1.2582 time to fit residues: 302.3961 Evaluate side-chains 229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 55 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103264 restraints weight = 12511.639| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.77 r_work: 0.3200 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9228 Z= 0.138 Angle : 0.566 14.108 12492 Z= 0.288 Chirality : 0.043 0.134 1422 Planarity : 0.004 0.042 1565 Dihedral : 4.614 60.067 1265 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.36 % Allowed : 21.92 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1133 helix: 1.33 (0.27), residues: 406 sheet: -0.06 (0.30), residues: 278 loop : -0.65 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.020 0.001 PHE R 93 TYR 0.016 0.001 TYR B 111 ARG 0.007 0.001 ARG R 54 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 427) hydrogen bonds : angle 4.61255 ( 1218) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.57380 ( 6) covalent geometry : bond 0.00321 ( 9225) covalent geometry : angle 0.56614 (12486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8454.34 seconds wall clock time: 150 minutes 7.31 seconds (9007.31 seconds total)