Starting phenix.real_space_refine on Tue Jul 29 22:18:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7j_39816/07_2025/8z7j_39816.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7j_39816/07_2025/8z7j_39816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7j_39816/07_2025/8z7j_39816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7j_39816/07_2025/8z7j_39816.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7j_39816/07_2025/8z7j_39816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7j_39816/07_2025/8z7j_39816.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2113 atoms to isotropic. 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 78 5.16 5 C 6396 2.51 5 N 1710 2.21 5 O 1905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10089 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1819 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 457 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2435 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain: "S" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 971 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Time building chain proxies: 6.11, per 1000 atoms: 0.61 Number of scatterers: 10089 At special positions: 0 Unit cell: (89.44, 121.68, 160.16, 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 78 16.00 O 1905 8.00 N 1710 7.00 C 6396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.03 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 95 " distance=2.03 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 110 " 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: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 37.2% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.041A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.771A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.056A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.115A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix 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 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 35 through 55 Processing helix chain 'C' and resid 60 through 76 Processing helix chain 'R' and resid 24 through 28 Processing helix chain 'R' and resid 29 through 61 removed outlier: 3.738A pdb=" N ALA R 33 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ARG R 58 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU R 59 " --> pdb=" O ARG R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.619A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 3.801A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 132 Processing helix chain 'R' and resid 136 through 145 removed outlier: 5.701A pdb=" N ARG R 143 " --> pdb=" O ARG R 139 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL R 144 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 168 removed outlier: 4.203A pdb=" N THR R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 193 through 210 Processing helix chain 'R' and resid 210 through 232 removed outlier: 3.532A pdb=" N THR R 215 " --> pdb=" O VAL R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 275 removed outlier: 4.369A pdb=" N MET R 262 " --> pdb=" O ALA R 258 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 280 through 310 Proline residue: R 292 - end of helix removed outlier: 3.559A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 321 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.924A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.068A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 90 Processing helix chain 'N' and resid 111 through 115 removed outlier: 3.574A pdb=" N MET N 114 " --> pdb=" O LYS N 111 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS N 115 " --> pdb=" O TRP N 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 111 through 115' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.626A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.506A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.625A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.486A 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: 4.244A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.762A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.261A 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: 6.693A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.999A 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: 6.602A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.921A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.883A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 149 removed outlier: 3.552A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.873A pdb=" N LEU N 18 " --> pdb=" O MET N 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.937A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N MET N 34 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER N 119 " --> pdb=" O ALA N 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.937A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N MET N 34 " --> pdb=" O LEU N 50 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1389 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: 3.41 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3252 1.34 - 1.46: 2586 1.46 - 1.59: 4352 1.59 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 10304 Sorted by residual: bond pdb=" N ILE B 269 " pdb=" CA ILE B 269 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.17e-02 7.31e+03 8.65e+00 bond pdb=" N CYS B 271 " pdb=" CA CYS B 271 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 8.01e+00 bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.78e+00 bond pdb=" C CYS B 271 " pdb=" O CYS B 271 " ideal model delta sigma weight residual 1.234 1.250 -0.016 1.17e-02 7.31e+03 1.91e+00 bond pdb=" C ILE B 269 " pdb=" O ILE B 269 " ideal model delta sigma weight residual 1.237 1.250 -0.014 9.90e-03 1.02e+04 1.90e+00 ... (remaining 10299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 13769 2.42 - 4.85: 149 4.85 - 7.27: 30 7.27 - 9.69: 7 9.69 - 12.12: 1 Bond angle restraints: 13956 Sorted by residual: angle pdb=" CB MET N 82 " pdb=" CG MET N 82 " pdb=" SD MET N 82 " ideal model delta sigma weight residual 112.70 124.82 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" CA GLN N 39 " pdb=" CB GLN N 39 " pdb=" CG GLN N 39 " ideal model delta sigma weight residual 114.10 121.73 -7.63 2.00e+00 2.50e-01 1.45e+01 angle pdb=" N SER B 227 " pdb=" CA SER B 227 " pdb=" C SER B 227 " ideal model delta sigma weight residual 108.34 112.91 -4.57 1.31e+00 5.83e-01 1.22e+01 angle pdb=" N TYR S 235 " pdb=" CA TYR S 235 " pdb=" C TYR S 235 " ideal model delta sigma weight residual 109.81 117.18 -7.37 2.21e+00 2.05e-01 1.11e+01 angle pdb=" CB MET R 113 " pdb=" CG MET R 113 " pdb=" SD MET R 113 " ideal model delta sigma weight residual 112.70 103.04 9.66 3.00e+00 1.11e-01 1.04e+01 ... (remaining 13951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 5308 17.57 - 35.15: 602 35.15 - 52.72: 148 52.72 - 70.29: 34 70.29 - 87.87: 9 Dihedral angle restraints: 6101 sinusoidal: 2360 harmonic: 3741 Sorted by residual: dihedral pdb=" CB CYS N 33 " pdb=" SG CYS N 33 " pdb=" SG CYS N 110 " pdb=" CB CYS N 110 " ideal model delta sinusoidal sigma weight residual -86.00 -172.09 86.09 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 95 " pdb=" CB CYS N 95 " ideal model delta sinusoidal sigma weight residual 93.00 45.55 47.45 1 1.00e+01 1.00e-02 3.11e+01 ... (remaining 6098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1262 0.051 - 0.103: 256 0.103 - 0.154: 42 0.154 - 0.205: 4 0.205 - 0.256: 3 Chirality restraints: 1567 Sorted by residual: chirality pdb=" CB THR S 91 " pdb=" CA THR S 91 " pdb=" OG1 THR S 91 " pdb=" CG2 THR S 91 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE B 270 " pdb=" N ILE B 270 " pdb=" C ILE B 270 " pdb=" CB ILE B 270 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1564 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO S 75 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN N 39 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" CD GLN N 39 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN N 39 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN N 39 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP R 279 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO R 280 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO R 280 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 280 " -0.027 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 381 2.71 - 3.26: 10278 3.26 - 3.80: 17337 3.80 - 4.35: 22023 4.35 - 4.90: 36465 Nonbonded interactions: 86484 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.158 3.040 nonbonded pdb=" O VAL R 212 " pdb=" OG1 THR R 215 " model vdw 2.187 3.040 nonbonded pdb=" OD2 ASP B 290 " pdb=" NH2 ARG B 314 " model vdw 2.216 3.120 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 177 " model vdw 2.249 3.040 ... (remaining 86479 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.560 Find NCS groups from input model: 0.130 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10309 Z= 0.148 Angle : 0.662 12.117 13966 Z= 0.342 Chirality : 0.043 0.256 1567 Planarity : 0.005 0.068 1766 Dihedral : 15.966 87.867 3682 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 27.02 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1277 helix: 1.55 (0.26), residues: 413 sheet: -0.82 (0.28), residues: 329 loop : -1.20 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 85 HIS 0.002 0.001 HIS R 231 PHE 0.016 0.002 PHE R 291 TYR 0.030 0.002 TYR S 235 ARG 0.008 0.001 ARG N 66 Details of bonding type rmsd hydrogen bonds : bond 0.17176 ( 490) hydrogen bonds : angle 7.22755 ( 1389) SS BOND : bond 0.00263 ( 5) SS BOND : angle 1.27545 ( 10) covalent geometry : bond 0.00304 (10304) covalent geometry : angle 0.66148 (13956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7317 (mtt180) cc_final: 0.7081 (mtt180) REVERT: B 209 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7870 (mtpp) REVERT: B 246 ASP cc_start: 0.7683 (m-30) cc_final: 0.7419 (m-30) REVERT: S 43 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7883 (mmtt) REVERT: N 51 MET cc_start: 0.6542 (tpp) cc_final: 0.6335 (tpp) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2435 time to fit residues: 94.3451 Evaluate side-chains 282 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.5980 chunk 96 optimal weight: 0.0050 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 74 optimal weight: 0.0470 chunk 115 optimal weight: 30.0000 overall best weight: 0.1870 ------------------------------------------------------------------------------- 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** N 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.165404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137124 restraints weight = 15546.872| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.31 r_work: 0.3596 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10309 Z= 0.117 Angle : 0.588 9.380 13966 Z= 0.305 Chirality : 0.041 0.230 1567 Planarity : 0.004 0.049 1766 Dihedral : 4.747 81.077 1406 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.55 % Allowed : 22.20 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.19 (0.24), residues: 1277 helix: 1.58 (0.25), residues: 416 sheet: -0.57 (0.28), residues: 329 loop : -1.18 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.003 0.001 HIS R 231 PHE 0.011 0.001 PHE R 210 TYR 0.031 0.002 TYR S 235 ARG 0.007 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 490) hydrogen bonds : angle 5.28971 ( 1389) SS BOND : bond 0.00271 ( 5) SS BOND : angle 1.37432 ( 10) covalent geometry : bond 0.00249 (10304) covalent geometry : angle 0.58684 (13956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 293 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7754 (ptp90) cc_final: 0.7408 (ptp90) REVERT: A 240 MET cc_start: 0.7147 (mmm) cc_final: 0.6662 (mmm) REVERT: A 262 THR cc_start: 0.8219 (p) cc_final: 0.7972 (m) REVERT: A 341 ASP cc_start: 0.8195 (t70) cc_final: 0.7793 (t70) REVERT: B 68 ARG cc_start: 0.8300 (ttt180) cc_final: 0.8076 (ttt180) REVERT: B 150 ARG cc_start: 0.8228 (mmt-90) cc_final: 0.7601 (mpt180) REVERT: B 170 ASP cc_start: 0.7959 (m-30) cc_final: 0.7753 (m-30) REVERT: B 198 LEU cc_start: 0.8160 (mp) cc_final: 0.7920 (mt) REVERT: B 264 TYR cc_start: 0.8335 (m-80) cc_final: 0.8077 (m-80) REVERT: B 290 ASP cc_start: 0.7298 (m-30) cc_final: 0.7032 (m-30) REVERT: R 76 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7403 (mp) REVERT: R 140 LEU cc_start: 0.3643 (OUTLIER) cc_final: 0.3408 (mm) REVERT: R 165 MET cc_start: 0.7244 (tpt) cc_final: 0.6980 (tpt) REVERT: R 167 LEU cc_start: 0.7885 (mt) cc_final: 0.7678 (mt) REVERT: R 178 LYS cc_start: 0.7897 (mttm) cc_final: 0.7280 (mttm) REVERT: S 5 VAL cc_start: 0.8444 (t) cc_final: 0.8101 (p) REVERT: S 43 LYS cc_start: 0.8261 (mmtt) cc_final: 0.8020 (mmtt) REVERT: S 67 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7996 (mtp85) REVERT: S 95 TYR cc_start: 0.8458 (m-80) cc_final: 0.8221 (m-80) REVERT: S 235 TYR cc_start: 0.5933 (OUTLIER) cc_final: 0.5315 (t80) outliers start: 50 outliers final: 27 residues processed: 322 average time/residue: 0.2440 time to fit residues: 106.7273 Evaluate side-chains 311 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 19 optimal weight: 0.6980 chunk 97 optimal weight: 0.0670 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 155 ASN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.163623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134640 restraints weight = 15769.992| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.35 r_work: 0.3553 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10309 Z= 0.151 Angle : 0.571 8.320 13966 Z= 0.300 Chirality : 0.041 0.249 1567 Planarity : 0.004 0.042 1766 Dihedral : 4.638 67.412 1406 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.10 % Allowed : 23.38 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1277 helix: 1.68 (0.25), residues: 414 sheet: -0.56 (0.27), residues: 328 loop : -1.17 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS R 265 PHE 0.013 0.001 PHE S 239 TYR 0.035 0.002 TYR S 235 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 490) hydrogen bonds : angle 5.08778 ( 1389) SS BOND : bond 0.00276 ( 5) SS BOND : angle 1.11636 ( 10) covalent geometry : bond 0.00334 (10304) covalent geometry : angle 0.57021 (13956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 240 MET cc_start: 0.7178 (mmm) cc_final: 0.6674 (mmm) REVERT: A 341 ASP cc_start: 0.8231 (t70) cc_final: 0.7778 (t70) REVERT: A 345 LYS cc_start: 0.8497 (mmtp) cc_final: 0.8288 (mmtm) REVERT: B 48 ARG cc_start: 0.8313 (mmt-90) cc_final: 0.8093 (mmt90) REVERT: B 150 ARG cc_start: 0.8233 (mmt-90) cc_final: 0.7911 (mmt-90) REVERT: B 198 LEU cc_start: 0.8210 (mp) cc_final: 0.7973 (mt) REVERT: B 290 ASP cc_start: 0.7351 (m-30) cc_final: 0.6916 (m-30) REVERT: R 101 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7379 (t80) REVERT: R 140 LEU cc_start: 0.3710 (OUTLIER) cc_final: 0.3446 (mm) REVERT: R 165 MET cc_start: 0.7233 (tpt) cc_final: 0.6953 (tpt) REVERT: R 167 LEU cc_start: 0.7923 (mt) cc_final: 0.7688 (mt) REVERT: R 178 LYS cc_start: 0.7899 (mttm) cc_final: 0.7333 (mttm) REVERT: R 210 PHE cc_start: 0.7661 (t80) cc_final: 0.7310 (t80) REVERT: S 43 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8060 (mmtt) REVERT: S 59 TYR cc_start: 0.7340 (m-10) cc_final: 0.7110 (m-10) REVERT: S 67 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7974 (mtp85) REVERT: S 95 TYR cc_start: 0.8523 (m-80) cc_final: 0.8302 (m-80) REVERT: S 235 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.5414 (t80) REVERT: N 105 TYR cc_start: 0.6875 (m-80) cc_final: 0.6523 (m-80) outliers start: 56 outliers final: 30 residues processed: 326 average time/residue: 0.2361 time to fit residues: 104.6274 Evaluate side-chains 325 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 291 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 212 PHE Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 176 GLN B 239 ASN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.163616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.134637 restraints weight = 15586.541| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.33 r_work: 0.3551 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10309 Z= 0.145 Angle : 0.575 10.546 13966 Z= 0.296 Chirality : 0.042 0.245 1567 Planarity : 0.004 0.042 1766 Dihedral : 4.649 67.853 1406 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.64 % Allowed : 24.48 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1277 helix: 1.64 (0.25), residues: 417 sheet: -0.59 (0.27), residues: 328 loop : -1.14 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.002 0.001 HIS R 265 PHE 0.013 0.001 PHE R 39 TYR 0.034 0.002 TYR S 235 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 490) hydrogen bonds : angle 4.98689 ( 1389) SS BOND : bond 0.00454 ( 5) SS BOND : angle 1.06670 ( 10) covalent geometry : bond 0.00321 (10304) covalent geometry : angle 0.57403 (13956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 300 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7177 (mmm) cc_final: 0.6653 (mmm) REVERT: A 335 VAL cc_start: 0.7859 (t) cc_final: 0.7619 (t) REVERT: A 341 ASP cc_start: 0.8250 (t70) cc_final: 0.7949 (t70) REVERT: B 48 ARG cc_start: 0.8317 (mmt-90) cc_final: 0.8087 (mmt90) REVERT: B 59 TYR cc_start: 0.8158 (m-80) cc_final: 0.7957 (m-80) REVERT: B 74 SER cc_start: 0.8481 (p) cc_final: 0.8239 (t) REVERT: B 119 ASN cc_start: 0.8175 (m-40) cc_final: 0.7929 (m-40) REVERT: B 150 ARG cc_start: 0.8228 (mmt-90) cc_final: 0.7896 (mmt-90) REVERT: B 170 ASP cc_start: 0.7846 (m-30) cc_final: 0.7597 (m-30) REVERT: B 290 ASP cc_start: 0.7263 (m-30) cc_final: 0.6762 (m-30) REVERT: B 314 ARG cc_start: 0.8046 (ptp-170) cc_final: 0.7773 (ptp-170) REVERT: R 140 LEU cc_start: 0.3399 (OUTLIER) cc_final: 0.3156 (mm) REVERT: R 165 MET cc_start: 0.7222 (tpt) cc_final: 0.6907 (tpt) REVERT: R 167 LEU cc_start: 0.7900 (mt) cc_final: 0.7673 (mt) REVERT: R 178 LYS cc_start: 0.7912 (mttm) cc_final: 0.7338 (mttm) REVERT: R 210 PHE cc_start: 0.7700 (t80) cc_final: 0.7451 (t80) REVERT: R 232 PHE cc_start: 0.7597 (m-80) cc_final: 0.7114 (m-80) REVERT: R 302 SER cc_start: 0.7772 (p) cc_final: 0.7353 (t) REVERT: S 43 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8072 (mmtt) REVERT: S 59 TYR cc_start: 0.7395 (m-10) cc_final: 0.7122 (m-10) REVERT: S 235 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.5438 (t80) outliers start: 51 outliers final: 36 residues processed: 325 average time/residue: 0.2256 time to fit residues: 100.5292 Evaluate side-chains 336 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 298 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 212 PHE Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 92 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 106 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.0170 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.163391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134585 restraints weight = 15517.809| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.33 r_work: 0.3548 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10309 Z= 0.135 Angle : 0.561 8.989 13966 Z= 0.291 Chirality : 0.041 0.234 1567 Planarity : 0.004 0.042 1766 Dihedral : 4.626 68.411 1406 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.46 % Allowed : 25.66 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1277 helix: 1.69 (0.25), residues: 416 sheet: -0.60 (0.27), residues: 328 loop : -1.15 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS S 35 PHE 0.021 0.001 PHE R 312 TYR 0.033 0.002 TYR S 235 ARG 0.008 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 490) hydrogen bonds : angle 4.83522 ( 1389) SS BOND : bond 0.00207 ( 5) SS BOND : angle 1.08692 ( 10) covalent geometry : bond 0.00301 (10304) covalent geometry : angle 0.56019 (13956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7144 (mmm) cc_final: 0.6611 (mmm) REVERT: A 335 VAL cc_start: 0.7883 (t) cc_final: 0.7627 (t) REVERT: B 48 ARG cc_start: 0.8312 (mmt-90) cc_final: 0.8070 (mmt90) REVERT: B 59 TYR cc_start: 0.8155 (m-80) cc_final: 0.7918 (m-80) REVERT: B 74 SER cc_start: 0.8468 (p) cc_final: 0.8234 (t) REVERT: B 119 ASN cc_start: 0.8224 (m-40) cc_final: 0.8019 (m-40) REVERT: B 150 ARG cc_start: 0.8215 (mmt-90) cc_final: 0.7877 (mmt-90) REVERT: B 170 ASP cc_start: 0.7866 (m-30) cc_final: 0.7545 (m-30) REVERT: R 140 LEU cc_start: 0.3390 (OUTLIER) cc_final: 0.3161 (mm) REVERT: R 165 MET cc_start: 0.7243 (tpt) cc_final: 0.6915 (tpt) REVERT: R 167 LEU cc_start: 0.7925 (mt) cc_final: 0.7702 (mt) REVERT: R 178 LYS cc_start: 0.7868 (mttm) cc_final: 0.7355 (mttm) REVERT: R 210 PHE cc_start: 0.7682 (t80) cc_final: 0.7475 (t80) REVERT: R 302 SER cc_start: 0.7780 (p) cc_final: 0.7361 (t) REVERT: R 309 TYR cc_start: 0.8056 (m-80) cc_final: 0.7587 (m-80) REVERT: S 43 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8054 (mmtt) REVERT: S 67 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7939 (mtp85) REVERT: S 235 TYR cc_start: 0.5954 (OUTLIER) cc_final: 0.5450 (t80) outliers start: 49 outliers final: 38 residues processed: 326 average time/residue: 0.3095 time to fit residues: 140.5521 Evaluate side-chains 343 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 302 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 212 PHE Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 92 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 176 GLN B 230 ASN S 82 GLN S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.160931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.131777 restraints weight = 15626.941| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.34 r_work: 0.3517 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10309 Z= 0.206 Angle : 0.626 10.871 13966 Z= 0.324 Chirality : 0.043 0.267 1567 Planarity : 0.004 0.042 1766 Dihedral : 4.815 68.555 1406 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.82 % Allowed : 26.30 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.17 (0.24), residues: 1277 helix: 1.67 (0.25), residues: 415 sheet: -0.73 (0.27), residues: 337 loop : -1.09 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS R 265 PHE 0.018 0.002 PHE R 312 TYR 0.043 0.002 TYR S 235 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 490) hydrogen bonds : angle 4.96569 ( 1389) SS BOND : bond 0.00279 ( 5) SS BOND : angle 1.20734 ( 10) covalent geometry : bond 0.00459 (10304) covalent geometry : angle 0.62569 (13956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 311 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7149 (mmm) cc_final: 0.6607 (mmm) REVERT: B 33 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7912 (mm) REVERT: B 48 ARG cc_start: 0.8342 (mmt-90) cc_final: 0.8122 (mmt90) REVERT: B 59 TYR cc_start: 0.8226 (m-80) cc_final: 0.7941 (m-80) REVERT: B 130 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7816 (mm-30) REVERT: B 150 ARG cc_start: 0.8203 (mmt-90) cc_final: 0.7982 (mmt-90) REVERT: B 228 ASP cc_start: 0.7563 (m-30) cc_final: 0.7333 (m-30) REVERT: R 140 LEU cc_start: 0.3401 (OUTLIER) cc_final: 0.3168 (mm) REVERT: R 165 MET cc_start: 0.7321 (tpt) cc_final: 0.7025 (tpt) REVERT: R 178 LYS cc_start: 0.8000 (mttm) cc_final: 0.7534 (mttm) REVERT: R 302 SER cc_start: 0.7820 (p) cc_final: 0.7544 (t) REVERT: S 43 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8083 (mmtt) REVERT: S 67 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8017 (mtp85) REVERT: S 235 TYR cc_start: 0.6142 (OUTLIER) cc_final: 0.5575 (t80) outliers start: 53 outliers final: 38 residues processed: 339 average time/residue: 0.2338 time to fit residues: 108.7815 Evaluate side-chains 348 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 212 PHE Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 92 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 88 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.160431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131051 restraints weight = 15731.761| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.35 r_work: 0.3504 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10309 Z= 0.225 Angle : 0.635 10.679 13966 Z= 0.328 Chirality : 0.044 0.272 1567 Planarity : 0.005 0.063 1766 Dihedral : 4.930 70.158 1406 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.82 % Allowed : 25.93 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.30 (0.24), residues: 1277 helix: 1.58 (0.25), residues: 414 sheet: -0.87 (0.26), residues: 336 loop : -1.13 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS B 54 PHE 0.020 0.002 PHE R 312 TYR 0.042 0.002 TYR S 235 ARG 0.007 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 490) hydrogen bonds : angle 5.02921 ( 1389) SS BOND : bond 0.00327 ( 5) SS BOND : angle 1.27052 ( 10) covalent geometry : bond 0.00502 (10304) covalent geometry : angle 0.63420 (13956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 307 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7203 (mmm) cc_final: 0.6659 (mmm) REVERT: A 345 LYS cc_start: 0.8543 (mmtp) cc_final: 0.8323 (mmtm) REVERT: B 48 ARG cc_start: 0.8329 (mmt-90) cc_final: 0.8113 (mmt90) REVERT: B 59 TYR cc_start: 0.8212 (m-80) cc_final: 0.7903 (m-80) REVERT: B 130 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 150 ARG cc_start: 0.8219 (mmt-90) cc_final: 0.7996 (mmt-90) REVERT: B 170 ASP cc_start: 0.7870 (m-30) cc_final: 0.7653 (m-30) REVERT: B 228 ASP cc_start: 0.7672 (m-30) cc_final: 0.7367 (m-30) REVERT: B 290 ASP cc_start: 0.7360 (m-30) cc_final: 0.6863 (t0) REVERT: B 314 ARG cc_start: 0.8122 (ptp-170) cc_final: 0.7748 (ptp-170) REVERT: R 140 LEU cc_start: 0.3408 (OUTLIER) cc_final: 0.3171 (mm) REVERT: R 165 MET cc_start: 0.7346 (tpt) cc_final: 0.7049 (tpt) REVERT: R 178 LYS cc_start: 0.8040 (mttm) cc_final: 0.7594 (mttm) REVERT: R 216 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7487 (mp) REVERT: R 302 SER cc_start: 0.7817 (p) cc_final: 0.7413 (t) REVERT: S 67 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8031 (mtp85) REVERT: S 235 TYR cc_start: 0.6197 (OUTLIER) cc_final: 0.5660 (t80) REVERT: N 44 GLU cc_start: 0.5601 (OUTLIER) cc_final: 0.5352 (tm-30) outliers start: 53 outliers final: 38 residues processed: 335 average time/residue: 0.2720 time to fit residues: 124.3180 Evaluate side-chains 348 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 301 ASN Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 212 PHE Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 44 GLU Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 92 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 58 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.161857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.132665 restraints weight = 15732.794| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.35 r_work: 0.3532 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10309 Z= 0.147 Angle : 0.601 9.024 13966 Z= 0.309 Chirality : 0.042 0.246 1567 Planarity : 0.004 0.042 1766 Dihedral : 4.825 73.129 1406 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.37 % Allowed : 26.66 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1277 helix: 1.69 (0.25), residues: 414 sheet: -0.71 (0.27), residues: 332 loop : -1.19 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.002 0.001 HIS S 35 PHE 0.018 0.001 PHE R 312 TYR 0.035 0.002 TYR S 235 ARG 0.007 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 490) hydrogen bonds : angle 4.91105 ( 1389) SS BOND : bond 0.00233 ( 5) SS BOND : angle 1.13603 ( 10) covalent geometry : bond 0.00330 (10304) covalent geometry : angle 0.60039 (13956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 312 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7188 (mmm) cc_final: 0.6702 (mmm) REVERT: B 33 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7863 (mm) REVERT: B 48 ARG cc_start: 0.8324 (mmt-90) cc_final: 0.8092 (mmt90) REVERT: B 59 TYR cc_start: 0.8204 (m-80) cc_final: 0.7892 (m-80) REVERT: B 130 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7822 (mm-30) REVERT: B 150 ARG cc_start: 0.8225 (mmt-90) cc_final: 0.7865 (mmt-90) REVERT: B 170 ASP cc_start: 0.7805 (m-30) cc_final: 0.7603 (m-30) REVERT: B 228 ASP cc_start: 0.7622 (m-30) cc_final: 0.7333 (m-30) REVERT: B 314 ARG cc_start: 0.8030 (ptp-170) cc_final: 0.7821 (ptp-170) REVERT: R 140 LEU cc_start: 0.3413 (OUTLIER) cc_final: 0.3178 (mm) REVERT: R 165 MET cc_start: 0.7307 (tpt) cc_final: 0.6991 (tpt) REVERT: R 178 LYS cc_start: 0.7885 (mttm) cc_final: 0.7514 (mttm) REVERT: R 216 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7520 (mt) REVERT: R 302 SER cc_start: 0.7782 (p) cc_final: 0.7369 (t) REVERT: S 6 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7237 (mm-30) REVERT: S 67 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7830 (mtp85) REVERT: S 87 ARG cc_start: 0.7812 (mtt-85) cc_final: 0.7427 (mtt-85) REVERT: S 235 TYR cc_start: 0.5961 (OUTLIER) cc_final: 0.5503 (t80) REVERT: N 44 GLU cc_start: 0.5334 (OUTLIER) cc_final: 0.5086 (tm-30) outliers start: 48 outliers final: 39 residues processed: 334 average time/residue: 0.3091 time to fit residues: 143.8361 Evaluate side-chains 350 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 301 ASN Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 212 PHE Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 44 GLU Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 92 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 59 optimal weight: 0.0370 chunk 104 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.162405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133132 restraints weight = 15798.511| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.36 r_work: 0.3523 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10309 Z= 0.156 Angle : 0.609 8.515 13966 Z= 0.314 Chirality : 0.042 0.244 1567 Planarity : 0.004 0.046 1766 Dihedral : 4.856 76.253 1406 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.64 % Allowed : 26.02 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1277 helix: 1.71 (0.26), residues: 414 sheet: -0.73 (0.27), residues: 332 loop : -1.19 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS B 54 PHE 0.017 0.001 PHE R 312 TYR 0.036 0.002 TYR S 235 ARG 0.007 0.000 ARG R 245 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 490) hydrogen bonds : angle 4.88520 ( 1389) SS BOND : bond 0.00244 ( 5) SS BOND : angle 1.15051 ( 10) covalent geometry : bond 0.00352 (10304) covalent geometry : angle 0.60811 (13956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 309 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7195 (mmm) cc_final: 0.6644 (mmm) REVERT: A 262 THR cc_start: 0.8314 (p) cc_final: 0.8097 (m) REVERT: A 312 LYS cc_start: 0.8257 (mttp) cc_final: 0.7959 (mttp) REVERT: B 17 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: B 33 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7863 (mm) REVERT: B 48 ARG cc_start: 0.8336 (mmt-90) cc_final: 0.8105 (mmt90) REVERT: B 59 TYR cc_start: 0.8210 (m-80) cc_final: 0.7904 (m-80) REVERT: B 129 ARG cc_start: 0.8219 (mtp85) cc_final: 0.8009 (mmm160) REVERT: B 130 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 170 ASP cc_start: 0.7830 (m-30) cc_final: 0.7580 (m-30) REVERT: B 228 ASP cc_start: 0.7629 (m-30) cc_final: 0.7342 (m-30) REVERT: R 140 LEU cc_start: 0.3411 (OUTLIER) cc_final: 0.3181 (mm) REVERT: R 165 MET cc_start: 0.7308 (tpt) cc_final: 0.6977 (tpt) REVERT: R 178 LYS cc_start: 0.7894 (mttm) cc_final: 0.7624 (mttm) REVERT: R 302 SER cc_start: 0.7779 (p) cc_final: 0.7442 (t) REVERT: S 43 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8067 (mmtt) REVERT: S 87 ARG cc_start: 0.7772 (mtt-85) cc_final: 0.7429 (mtt-85) REVERT: S 235 TYR cc_start: 0.6021 (OUTLIER) cc_final: 0.5514 (t80) REVERT: N 44 GLU cc_start: 0.5312 (OUTLIER) cc_final: 0.5070 (tm-30) REVERT: N 59 TYR cc_start: 0.7915 (m-80) cc_final: 0.7558 (m-80) outliers start: 51 outliers final: 39 residues processed: 332 average time/residue: 0.2511 time to fit residues: 114.2713 Evaluate side-chains 350 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 306 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 301 ASN Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 212 PHE Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 44 GLU Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 92 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 109 optimal weight: 0.0270 chunk 52 optimal weight: 0.0370 chunk 72 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.163572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134431 restraints weight = 15770.245| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.35 r_work: 0.3550 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10309 Z= 0.129 Angle : 0.597 10.127 13966 Z= 0.306 Chirality : 0.042 0.225 1567 Planarity : 0.004 0.046 1766 Dihedral : 4.799 79.376 1406 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.91 % Allowed : 27.02 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1277 helix: 1.76 (0.26), residues: 415 sheet: -0.68 (0.27), residues: 331 loop : -1.16 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.024 0.001 PHE R 210 TYR 0.032 0.002 TYR S 235 ARG 0.008 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 490) hydrogen bonds : angle 4.81904 ( 1389) SS BOND : bond 0.00200 ( 5) SS BOND : angle 1.12081 ( 10) covalent geometry : bond 0.00290 (10304) covalent geometry : angle 0.59683 (13956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 309 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 LYS cc_start: 0.8265 (mttp) cc_final: 0.7984 (mttp) REVERT: A 317 LYS cc_start: 0.8291 (ptpp) cc_final: 0.7942 (ptmm) REVERT: A 335 VAL cc_start: 0.7893 (t) cc_final: 0.7631 (t) REVERT: B 17 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: B 33 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7796 (mm) REVERT: B 59 TYR cc_start: 0.8205 (m-80) cc_final: 0.7912 (m-80) REVERT: B 130 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7750 (mm-30) REVERT: B 170 ASP cc_start: 0.7805 (m-30) cc_final: 0.7570 (m-30) REVERT: B 228 ASP cc_start: 0.7629 (m-30) cc_final: 0.7379 (m-30) REVERT: R 140 LEU cc_start: 0.3405 (OUTLIER) cc_final: 0.3177 (mm) REVERT: R 165 MET cc_start: 0.7284 (tpt) cc_final: 0.6930 (tpt) REVERT: R 167 LEU cc_start: 0.7853 (mt) cc_final: 0.7649 (mt) REVERT: R 178 LYS cc_start: 0.7874 (mttm) cc_final: 0.7569 (mttm) REVERT: R 271 TYR cc_start: 0.5714 (t80) cc_final: 0.5240 (t80) REVERT: R 302 SER cc_start: 0.7730 (p) cc_final: 0.7435 (t) REVERT: S 43 LYS cc_start: 0.8323 (mmtt) cc_final: 0.8048 (mmtt) REVERT: S 223 ASP cc_start: 0.7821 (t70) cc_final: 0.7420 (t70) REVERT: S 235 TYR cc_start: 0.5878 (OUTLIER) cc_final: 0.5474 (t80) REVERT: N 44 GLU cc_start: 0.5227 (OUTLIER) cc_final: 0.4957 (tm-30) outliers start: 43 outliers final: 37 residues processed: 328 average time/residue: 0.2438 time to fit residues: 109.8188 Evaluate side-chains 346 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 212 PHE Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 44 GLU Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 92 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 70 optimal weight: 0.1980 chunk 75 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.162362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.133306 restraints weight = 15674.273| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.32 r_work: 0.3544 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10309 Z= 0.151 Angle : 0.621 9.680 13966 Z= 0.317 Chirality : 0.043 0.236 1567 Planarity : 0.004 0.060 1766 Dihedral : 4.887 82.609 1406 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.55 % Allowed : 27.57 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.24), residues: 1277 helix: 1.71 (0.26), residues: 416 sheet: -0.66 (0.27), residues: 331 loop : -1.17 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.024 0.001 PHE R 210 TYR 0.035 0.002 TYR S 235 ARG 0.011 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 490) hydrogen bonds : angle 4.82217 ( 1389) SS BOND : bond 0.00246 ( 5) SS BOND : angle 1.14984 ( 10) covalent geometry : bond 0.00342 (10304) covalent geometry : angle 0.62082 (13956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7422.65 seconds wall clock time: 135 minutes 10.13 seconds (8110.13 seconds total)