Starting phenix.real_space_refine on Wed Sep 17 22:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7j_39816/09_2025/8z7j_39816.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7j_39816/09_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_39816/09_2025/8z7j_39816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7j_39816/09_2025/8z7j_39816.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7j_39816/09_2025/8z7j_39816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7j_39816/09_2025/8z7j_39816.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLU: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: 2.64, per 1000 atoms: 0.26 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: 1.08 Conformation dependent library (CDL) restraints added in 400.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.43 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: 1.82 Time building geometry restraints manager: 1.39 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.750 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.870 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG N 66 TYR 0.030 0.002 TYR S 235 PHE 0.016 0.002 PHE R 291 TRP 0.025 0.002 TRP R 85 HIS 0.002 0.001 HIS R 231 Details of bonding type rmsd covalent geometry : bond 0.00304 (10304) covalent geometry : angle 0.66148 (13956) SS BOND : bond 0.00263 ( 5) SS BOND : angle 1.27545 ( 10) hydrogen bonds : bond 0.17176 ( 490) hydrogen bonds : angle 7.22755 ( 1389) *********************** 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 : 0.393 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: 0.1191 time to fit residues: 46.3327 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 : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 0.1980 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 75 GLN N 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.163066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133833 restraints weight = 15579.841| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.36 r_work: 0.3538 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10309 Z= 0.173 Angle : 0.615 8.703 13966 Z= 0.321 Chirality : 0.042 0.273 1567 Planarity : 0.004 0.051 1766 Dihedral : 4.892 79.793 1406 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.73 % Allowed : 22.57 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.24), residues: 1277 helix: 1.53 (0.26), residues: 415 sheet: -0.78 (0.27), residues: 349 loop : -1.13 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.039 0.002 TYR S 235 PHE 0.014 0.001 PHE S 239 TRP 0.022 0.002 TRP B 169 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00384 (10304) covalent geometry : angle 0.61421 (13956) SS BOND : bond 0.00349 ( 5) SS BOND : angle 1.55311 ( 10) hydrogen bonds : bond 0.04312 ( 490) hydrogen bonds : angle 5.47355 ( 1389) *********************** 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 348 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7192 (mmm) cc_final: 0.6711 (mmm) REVERT: B 48 ARG cc_start: 0.8324 (mmt-90) cc_final: 0.8003 (mmt-90) REVERT: B 119 ASN cc_start: 0.8214 (m-40) cc_final: 0.8001 (m-40) REVERT: B 290 ASP cc_start: 0.7475 (m-30) cc_final: 0.6940 (m-30) REVERT: R 76 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7518 (mp) REVERT: R 140 LEU cc_start: 0.3640 (OUTLIER) cc_final: 0.3403 (mm) REVERT: R 165 MET cc_start: 0.7218 (tpt) cc_final: 0.7014 (tpt) REVERT: R 178 LYS cc_start: 0.7943 (mttm) cc_final: 0.7361 (mttm) REVERT: R 217 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7525 (mtp) REVERT: S 43 LYS cc_start: 0.8323 (mmtt) cc_final: 0.8050 (mmtt) REVERT: S 67 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8001 (mtp85) REVERT: S 227 TYR cc_start: 0.7880 (m-80) cc_final: 0.7604 (m-80) REVERT: S 235 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5427 (t80) outliers start: 52 outliers final: 30 residues processed: 327 average time/residue: 0.1132 time to fit residues: 50.9681 Evaluate side-chains 319 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 65 THR 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 196 THR 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 109 ILE 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 217 MET 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 223 ASP 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 52 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 103 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 87 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.162365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133104 restraints weight = 15591.001| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.34 r_work: 0.3536 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10309 Z= 0.180 Angle : 0.594 8.510 13966 Z= 0.311 Chirality : 0.042 0.264 1567 Planarity : 0.004 0.044 1766 Dihedral : 4.898 77.036 1406 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.55 % Allowed : 23.29 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.24), residues: 1277 helix: 1.62 (0.25), residues: 413 sheet: -0.80 (0.26), residues: 352 loop : -1.08 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.038 0.002 TYR S 235 PHE 0.016 0.001 PHE S 239 TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00400 (10304) covalent geometry : angle 0.59322 (13956) SS BOND : bond 0.00304 ( 5) SS BOND : angle 1.29925 ( 10) hydrogen bonds : bond 0.04067 ( 490) hydrogen bonds : angle 5.22465 ( 1389) *********************** 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 361 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 300 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 240 MET cc_start: 0.7157 (mmm) cc_final: 0.6665 (mmm) REVERT: B 48 ARG cc_start: 0.8317 (mmt-90) cc_final: 0.8027 (mmt-90) REVERT: B 119 ASN cc_start: 0.8308 (m-40) cc_final: 0.8067 (m-40) REVERT: B 130 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7825 (mm-30) REVERT: B 150 ARG cc_start: 0.8216 (mmt-90) cc_final: 0.7812 (mmt-90) REVERT: B 290 ASP cc_start: 0.7405 (m-30) cc_final: 0.6818 (m-30) REVERT: B 314 ARG cc_start: 0.8066 (ptp-170) cc_final: 0.7775 (ptp-170) REVERT: R 101 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7452 (t80) REVERT: R 140 LEU cc_start: 0.3711 (OUTLIER) cc_final: 0.3445 (mm) REVERT: R 165 MET cc_start: 0.7264 (tpt) cc_final: 0.6981 (tpt) REVERT: R 167 LEU cc_start: 0.7924 (mt) cc_final: 0.7703 (mt) REVERT: R 178 LYS cc_start: 0.7931 (mttm) cc_final: 0.7388 (mttm) REVERT: R 216 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7533 (mp) REVERT: R 251 VAL cc_start: 0.8582 (m) cc_final: 0.8362 (p) REVERT: R 302 SER cc_start: 0.7719 (p) cc_final: 0.7243 (t) REVERT: S 43 LYS cc_start: 0.8362 (mmtt) cc_final: 0.8088 (mmtt) REVERT: S 227 TYR cc_start: 0.7909 (m-80) cc_final: 0.7558 (m-80) REVERT: S 235 TYR cc_start: 0.6199 (OUTLIER) cc_final: 0.5501 (t80) outliers start: 61 outliers final: 34 residues processed: 333 average time/residue: 0.1088 time to fit residues: 50.1012 Evaluate side-chains 334 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET 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 250 CYS 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 199 VAL 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 300 VAL 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 103 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 115 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 109 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.162967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133727 restraints weight = 15663.949| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.35 r_work: 0.3547 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10309 Z= 0.149 Angle : 0.594 10.605 13966 Z= 0.304 Chirality : 0.042 0.250 1567 Planarity : 0.004 0.044 1766 Dihedral : 4.833 77.832 1406 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.64 % Allowed : 24.02 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.24), residues: 1277 helix: 1.60 (0.25), residues: 417 sheet: -0.52 (0.28), residues: 326 loop : -1.18 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.036 0.002 TYR S 235 PHE 0.020 0.001 PHE R 312 TRP 0.017 0.002 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00331 (10304) covalent geometry : angle 0.59340 (13956) SS BOND : bond 0.00277 ( 5) SS BOND : angle 1.22071 ( 10) hydrogen bonds : bond 0.03837 ( 490) hydrogen bonds : angle 5.06045 ( 1389) *********************** 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 363 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 301 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 240 MET cc_start: 0.7170 (mmm) cc_final: 0.6647 (mmm) REVERT: A 317 LYS cc_start: 0.8357 (ptpp) cc_final: 0.7988 (ptmm) REVERT: A 335 VAL cc_start: 0.7889 (t) cc_final: 0.7640 (t) REVERT: B 74 SER cc_start: 0.8497 (p) cc_final: 0.8244 (t) REVERT: B 170 ASP cc_start: 0.7949 (m-30) cc_final: 0.7713 (m-30) REVERT: B 219 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7808 (ttm-80) REVERT: R 140 LEU cc_start: 0.3417 (OUTLIER) cc_final: 0.3172 (mm) REVERT: R 165 MET cc_start: 0.7300 (tpt) cc_final: 0.6978 (tpt) REVERT: R 167 LEU cc_start: 0.7926 (mt) cc_final: 0.7706 (mt) REVERT: R 178 LYS cc_start: 0.7919 (mttm) cc_final: 0.7354 (mttm) REVERT: R 302 SER cc_start: 0.7770 (p) cc_final: 0.7424 (t) REVERT: S 43 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8052 (mmtt) REVERT: S 67 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7953 (mtp85) REVERT: S 95 TYR cc_start: 0.8454 (m-80) cc_final: 0.8253 (m-80) REVERT: S 227 TYR cc_start: 0.7911 (m-80) cc_final: 0.7621 (m-80) REVERT: S 235 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.5411 (t80) outliers start: 62 outliers final: 42 residues processed: 338 average time/residue: 0.1125 time to fit residues: 52.9025 Evaluate side-chains 345 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 300 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET 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 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 250 CYS 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 R residue 262 MET Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 58 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 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 52 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 0.0020 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 0.0170 overall best weight: 0.5426 ------------------------------------------------------------------------------- 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 255 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.162890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.133843 restraints weight = 15760.581| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.35 r_work: 0.3543 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10309 Z= 0.143 Angle : 0.578 9.309 13966 Z= 0.299 Chirality : 0.042 0.241 1567 Planarity : 0.004 0.043 1766 Dihedral : 4.777 75.617 1406 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.91 % Allowed : 25.93 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.24), residues: 1277 helix: 1.69 (0.25), residues: 416 sheet: -0.56 (0.28), residues: 317 loop : -1.18 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.035 0.002 TYR S 235 PHE 0.013 0.001 PHE R 312 TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00317 (10304) covalent geometry : angle 0.57776 (13956) SS BOND : bond 0.00359 ( 5) SS BOND : angle 1.17993 ( 10) hydrogen bonds : bond 0.03697 ( 490) hydrogen bonds : angle 4.94198 ( 1389) *********************** 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 357 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 303 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7367 (mt-10) REVERT: A 240 MET cc_start: 0.7131 (mmm) cc_final: 0.6611 (mmm) REVERT: A 335 VAL cc_start: 0.7874 (t) cc_final: 0.7626 (t) REVERT: B 59 TYR cc_start: 0.8159 (m-80) cc_final: 0.7953 (m-80) REVERT: B 74 SER cc_start: 0.8501 (p) cc_final: 0.8244 (t) REVERT: B 130 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7822 (mm-30) REVERT: B 150 ARG cc_start: 0.8197 (mmt-90) cc_final: 0.7629 (mpt180) REVERT: B 219 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7798 (ttm-80) REVERT: R 71 LEU cc_start: 0.7967 (tp) cc_final: 0.7571 (tt) REVERT: R 140 LEU cc_start: 0.3400 (OUTLIER) cc_final: 0.3169 (mm) REVERT: R 165 MET cc_start: 0.7228 (tpt) cc_final: 0.6900 (tpt) REVERT: R 167 LEU cc_start: 0.7910 (mt) cc_final: 0.7690 (mt) REVERT: R 178 LYS cc_start: 0.7914 (mttm) cc_final: 0.7389 (mttm) REVERT: R 302 SER cc_start: 0.7775 (p) cc_final: 0.7433 (t) REVERT: S 43 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8058 (mmtt) REVERT: S 67 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8012 (mtp85) REVERT: S 227 TYR cc_start: 0.7902 (m-80) cc_final: 0.7590 (m-80) REVERT: S 235 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.5506 (t80) REVERT: N 105 TYR cc_start: 0.7030 (m-10) cc_final: 0.6617 (m-80) outliers start: 54 outliers final: 42 residues processed: 329 average time/residue: 0.1149 time to fit residues: 52.1134 Evaluate side-chains 345 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 300 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS 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 192 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 300 VAL Chi-restraints excluded: chain S residue 58 ILE 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 245 LEU 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 Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 12 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.162966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.133619 restraints weight = 15694.010| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.35 r_work: 0.3540 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10309 Z= 0.149 Angle : 0.583 9.482 13966 Z= 0.301 Chirality : 0.042 0.242 1567 Planarity : 0.004 0.043 1766 Dihedral : 4.765 75.836 1406 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 5.64 % Allowed : 24.66 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.24), residues: 1277 helix: 1.71 (0.25), residues: 415 sheet: -0.58 (0.27), residues: 326 loop : -1.17 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.036 0.002 TYR S 235 PHE 0.015 0.001 PHE A 274 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00332 (10304) covalent geometry : angle 0.58278 (13956) SS BOND : bond 0.00288 ( 5) SS BOND : angle 1.14112 ( 10) hydrogen bonds : bond 0.03684 ( 490) hydrogen bonds : angle 4.89880 ( 1389) *********************** 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 369 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 307 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.8185 (mt) cc_final: 0.7956 (mt) REVERT: A 240 MET cc_start: 0.7172 (mmm) cc_final: 0.6637 (mmm) REVERT: A 317 LYS cc_start: 0.8319 (ptpp) cc_final: 0.7985 (ptmm) REVERT: A 335 VAL cc_start: 0.7864 (t) cc_final: 0.7609 (t) REVERT: B 59 TYR cc_start: 0.8177 (m-80) cc_final: 0.7946 (m-80) REVERT: B 74 SER cc_start: 0.8495 (p) cc_final: 0.8243 (t) REVERT: B 130 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7777 (mm-30) REVERT: B 150 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7629 (mpt180) REVERT: B 170 ASP cc_start: 0.7846 (m-30) cc_final: 0.7631 (m-30) REVERT: R 71 LEU cc_start: 0.8061 (tp) cc_final: 0.7693 (tt) REVERT: R 140 LEU cc_start: 0.3415 (OUTLIER) cc_final: 0.3182 (mm) REVERT: R 165 MET cc_start: 0.7264 (tpt) cc_final: 0.6940 (tpt) REVERT: R 178 LYS cc_start: 0.7900 (mttm) cc_final: 0.7416 (mttm) REVERT: R 302 SER cc_start: 0.7764 (p) cc_final: 0.7483 (t) REVERT: S 43 LYS cc_start: 0.8350 (mmtt) cc_final: 0.8060 (mmtt) REVERT: S 67 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8037 (mtp85) REVERT: S 235 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.5502 (t80) REVERT: N 105 TYR cc_start: 0.7080 (m-10) cc_final: 0.6616 (m-80) outliers start: 62 outliers final: 41 residues processed: 340 average time/residue: 0.1109 time to fit residues: 52.3451 Evaluate side-chains 348 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 250 CYS 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 192 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 217 MET Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain S residue 58 ILE 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 62 SER Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 104 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.162320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133207 restraints weight = 15728.877| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.34 r_work: 0.3527 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10309 Z= 0.161 Angle : 0.591 9.328 13966 Z= 0.305 Chirality : 0.042 0.246 1567 Planarity : 0.004 0.042 1766 Dihedral : 4.812 77.419 1406 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.28 % Allowed : 25.20 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.24), residues: 1277 helix: 1.72 (0.25), residues: 416 sheet: -0.66 (0.27), residues: 317 loop : -1.16 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.037 0.002 TYR S 235 PHE 0.023 0.001 PHE R 312 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00360 (10304) covalent geometry : angle 0.58997 (13956) SS BOND : bond 0.00287 ( 5) SS BOND : angle 1.16467 ( 10) hydrogen bonds : bond 0.03722 ( 490) hydrogen bonds : angle 4.88633 ( 1389) *********************** 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 366 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 308 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.8183 (mt) cc_final: 0.7952 (mt) REVERT: A 240 MET cc_start: 0.7136 (mmm) cc_final: 0.6579 (mmm) REVERT: A 317 LYS cc_start: 0.8324 (ptpp) cc_final: 0.8012 (ptmm) REVERT: A 335 VAL cc_start: 0.7856 (t) cc_final: 0.7599 (t) REVERT: B 59 TYR cc_start: 0.8211 (m-80) cc_final: 0.7955 (m-80) REVERT: B 74 SER cc_start: 0.8496 (p) cc_final: 0.8249 (t) REVERT: B 130 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7809 (mm-30) REVERT: B 150 ARG cc_start: 0.8210 (mmt-90) cc_final: 0.7628 (mpt180) REVERT: B 170 ASP cc_start: 0.7865 (m-30) cc_final: 0.7597 (m-30) REVERT: B 228 ASP cc_start: 0.7592 (m-30) cc_final: 0.7354 (m-30) REVERT: R 71 LEU cc_start: 0.8073 (tp) cc_final: 0.7696 (tt) REVERT: R 140 LEU cc_start: 0.3414 (OUTLIER) cc_final: 0.3181 (mm) REVERT: R 165 MET cc_start: 0.7253 (tpt) cc_final: 0.6944 (tpt) REVERT: R 178 LYS cc_start: 0.7872 (mttm) cc_final: 0.7442 (mttm) REVERT: R 216 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7519 (mp) REVERT: R 302 SER cc_start: 0.7776 (p) cc_final: 0.7485 (t) REVERT: S 43 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8057 (mmtt) REVERT: S 67 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8004 (mtp85) REVERT: S 235 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.5509 (t80) REVERT: N 44 GLU cc_start: 0.5300 (OUTLIER) cc_final: 0.5067 (tm-30) outliers start: 58 outliers final: 42 residues processed: 337 average time/residue: 0.1129 time to fit residues: 52.7198 Evaluate side-chains 354 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 307 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 269 ASN 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 250 CYS 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 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 192 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 216 ILE Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain S residue 58 ILE 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 44 GLU Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 117 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.162456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133102 restraints weight = 15633.398| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.34 r_work: 0.3533 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10309 Z= 0.161 Angle : 0.590 9.041 13966 Z= 0.305 Chirality : 0.042 0.245 1567 Planarity : 0.004 0.042 1766 Dihedral : 4.839 79.035 1406 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.91 % Allowed : 24.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.24), residues: 1277 helix: 1.75 (0.25), residues: 415 sheet: -0.61 (0.27), residues: 324 loop : -1.18 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.037 0.002 TYR S 235 PHE 0.020 0.001 PHE R 312 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00358 (10304) covalent geometry : angle 0.58910 (13956) SS BOND : bond 0.00300 ( 5) SS BOND : angle 1.16164 ( 10) hydrogen bonds : bond 0.03708 ( 490) hydrogen bonds : angle 4.86040 ( 1389) *********************** 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 374 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 309 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.8214 (mt) cc_final: 0.7996 (mt) REVERT: A 240 MET cc_start: 0.7148 (mmm) cc_final: 0.6650 (mmm) REVERT: A 262 THR cc_start: 0.8352 (p) cc_final: 0.8006 (m) REVERT: A 312 LYS cc_start: 0.8208 (mttp) cc_final: 0.7976 (mttp) REVERT: A 317 LYS cc_start: 0.8328 (ptpp) cc_final: 0.7995 (ptmm) REVERT: A 335 VAL cc_start: 0.7870 (t) cc_final: 0.7606 (t) REVERT: B 33 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7883 (mm) REVERT: B 59 TYR cc_start: 0.8217 (m-80) cc_final: 0.7946 (m-80) REVERT: B 74 SER cc_start: 0.8495 (p) cc_final: 0.8249 (t) REVERT: B 129 ARG cc_start: 0.8218 (mtp85) cc_final: 0.8016 (mmm160) REVERT: B 130 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 150 ARG cc_start: 0.8209 (mmt-90) cc_final: 0.7617 (mpt180) REVERT: B 170 ASP cc_start: 0.7844 (m-30) cc_final: 0.7561 (m-30) REVERT: B 228 ASP cc_start: 0.7619 (m-30) cc_final: 0.7344 (m-30) REVERT: C 49 GLN cc_start: 0.8268 (tp-100) cc_final: 0.7968 (tp40) REVERT: R 71 LEU cc_start: 0.8069 (tp) cc_final: 0.7699 (tt) REVERT: R 140 LEU cc_start: 0.3393 (OUTLIER) cc_final: 0.3160 (mm) REVERT: R 165 MET cc_start: 0.7295 (tpt) cc_final: 0.6989 (tpt) REVERT: R 178 LYS cc_start: 0.7829 (mttm) cc_final: 0.7506 (mttm) REVERT: R 216 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7525 (mp) REVERT: R 302 SER cc_start: 0.7771 (p) cc_final: 0.7484 (t) REVERT: S 43 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8041 (mmtt) REVERT: S 223 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7297 (t70) REVERT: S 235 TYR cc_start: 0.6033 (OUTLIER) cc_final: 0.5501 (t80) REVERT: N 44 GLU cc_start: 0.5287 (OUTLIER) cc_final: 0.5047 (tm-30) outliers start: 65 outliers final: 47 residues processed: 342 average time/residue: 0.1100 time to fit residues: 52.3794 Evaluate side-chains 361 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 308 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 269 ASN 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 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP 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 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 192 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 216 ILE Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 301 ASN Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain S residue 58 ILE 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 44 GLU Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 38 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 26 optimal weight: 0.0010 chunk 104 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.163350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134000 restraints weight = 15681.937| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.35 r_work: 0.3543 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10309 Z= 0.136 Angle : 0.585 8.542 13966 Z= 0.301 Chirality : 0.042 0.232 1567 Planarity : 0.004 0.042 1766 Dihedral : 4.818 81.572 1406 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.91 % Allowed : 26.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.24), residues: 1277 helix: 1.75 (0.25), residues: 415 sheet: -0.62 (0.27), residues: 329 loop : -1.17 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 67 TYR 0.034 0.002 TYR S 235 PHE 0.019 0.001 PHE R 312 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00303 (10304) covalent geometry : angle 0.58396 (13956) SS BOND : bond 0.00250 ( 5) SS BOND : angle 1.21506 ( 10) hydrogen bonds : bond 0.03643 ( 490) hydrogen bonds : angle 4.80947 ( 1389) *********************** 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 362 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 308 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.8227 (mt) cc_final: 0.8012 (mt) REVERT: A 240 MET cc_start: 0.7150 (mmm) cc_final: 0.6613 (mmm) REVERT: A 262 THR cc_start: 0.8324 (p) cc_final: 0.8025 (m) REVERT: A 312 LYS cc_start: 0.8239 (mttp) cc_final: 0.8039 (mttp) REVERT: A 317 LYS cc_start: 0.8302 (ptpp) cc_final: 0.7966 (ptmm) REVERT: A 335 VAL cc_start: 0.7892 (t) cc_final: 0.7632 (t) REVERT: B 33 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7807 (mm) REVERT: B 59 TYR cc_start: 0.8205 (m-80) cc_final: 0.7932 (m-80) REVERT: B 74 SER cc_start: 0.8471 (p) cc_final: 0.8238 (t) REVERT: B 119 ASN cc_start: 0.8293 (m-40) cc_final: 0.8028 (m-40) REVERT: B 130 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7762 (mm-30) REVERT: B 150 ARG cc_start: 0.8210 (mmt-90) cc_final: 0.7639 (mpt180) REVERT: B 170 ASP cc_start: 0.7853 (m-30) cc_final: 0.7568 (m-30) REVERT: B 228 ASP cc_start: 0.7636 (m-30) cc_final: 0.7387 (m-30) REVERT: R 71 LEU cc_start: 0.8103 (tp) cc_final: 0.7742 (tt) REVERT: R 140 LEU cc_start: 0.3417 (OUTLIER) cc_final: 0.3185 (mm) REVERT: R 165 MET cc_start: 0.7250 (tpt) cc_final: 0.6924 (tpt) REVERT: R 178 LYS cc_start: 0.7843 (mttm) cc_final: 0.7498 (mttm) REVERT: R 302 SER cc_start: 0.7728 (p) cc_final: 0.7469 (t) REVERT: S 43 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8051 (mmtt) REVERT: S 223 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7280 (t70) REVERT: S 235 TYR cc_start: 0.5957 (OUTLIER) cc_final: 0.5488 (t80) REVERT: N 44 GLU cc_start: 0.5200 (OUTLIER) cc_final: 0.4937 (tm-30) outliers start: 54 outliers final: 45 residues processed: 333 average time/residue: 0.1093 time to fit residues: 50.2569 Evaluate side-chains 357 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 307 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 269 ASN 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 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP 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 67 PHE Chi-restraints excluded: chain R residue 97 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 192 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 262 MET Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain S residue 58 ILE 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 44 GLU Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 82 MET 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 93 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 45 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.163198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133652 restraints weight = 15470.904| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.37 r_work: 0.3538 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10309 Z= 0.153 Angle : 0.601 8.515 13966 Z= 0.309 Chirality : 0.042 0.239 1567 Planarity : 0.004 0.043 1766 Dihedral : 4.863 81.997 1406 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.73 % Allowed : 26.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.24), residues: 1277 helix: 1.69 (0.25), residues: 416 sheet: -0.64 (0.27), residues: 324 loop : -1.20 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 22 TYR 0.036 0.002 TYR S 235 PHE 0.021 0.002 PHE R 210 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00343 (10304) covalent geometry : angle 0.60027 (13956) SS BOND : bond 0.00250 ( 5) SS BOND : angle 1.20027 ( 10) hydrogen bonds : bond 0.03651 ( 490) hydrogen bonds : angle 4.81412 ( 1389) ********************** 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 360 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 308 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.8214 (mt) cc_final: 0.8008 (mt) REVERT: A 240 MET cc_start: 0.7159 (mmm) cc_final: 0.6621 (mmm) REVERT: A 262 THR cc_start: 0.8316 (p) cc_final: 0.8073 (m) REVERT: A 312 LYS cc_start: 0.8247 (mttp) cc_final: 0.8041 (mttp) REVERT: A 317 LYS cc_start: 0.8330 (ptpp) cc_final: 0.7988 (ptmm) REVERT: A 335 VAL cc_start: 0.7883 (t) cc_final: 0.7623 (t) REVERT: B 33 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7812 (mm) REVERT: B 59 TYR cc_start: 0.8216 (m-80) cc_final: 0.7932 (m-80) REVERT: B 74 SER cc_start: 0.8498 (p) cc_final: 0.8254 (t) REVERT: B 130 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7808 (mm-30) REVERT: B 150 ARG cc_start: 0.8211 (mmt-90) cc_final: 0.7641 (mpt180) REVERT: B 170 ASP cc_start: 0.7855 (m-30) cc_final: 0.7560 (m-30) REVERT: B 197 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7847 (mtt180) REVERT: B 228 ASP cc_start: 0.7677 (m-30) cc_final: 0.7416 (m-30) REVERT: C 49 GLN cc_start: 0.8203 (tp-100) cc_final: 0.7984 (tp40) REVERT: R 71 LEU cc_start: 0.8098 (tp) cc_final: 0.7721 (tt) REVERT: R 140 LEU cc_start: 0.3391 (OUTLIER) cc_final: 0.3162 (mm) REVERT: R 165 MET cc_start: 0.7270 (tpt) cc_final: 0.6938 (tpt) REVERT: R 178 LYS cc_start: 0.7870 (mttm) cc_final: 0.7545 (mttm) REVERT: R 302 SER cc_start: 0.7763 (p) cc_final: 0.7529 (t) REVERT: S 43 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8053 (mmtt) REVERT: S 223 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7293 (t70) REVERT: S 235 TYR cc_start: 0.5992 (OUTLIER) cc_final: 0.5499 (t80) REVERT: N 44 GLU cc_start: 0.5225 (OUTLIER) cc_final: 0.4947 (tm-30) REVERT: N 51 MET cc_start: 0.6895 (tpp) cc_final: 0.6665 (tpp) outliers start: 52 outliers final: 43 residues processed: 331 average time/residue: 0.1071 time to fit residues: 49.3192 Evaluate side-chains 354 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 306 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 269 ASN 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 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS 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 67 PHE Chi-restraints excluded: chain R residue 97 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 192 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 217 MET 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 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 44 GLU Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 104 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 99 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 106 optimal weight: 0.0050 chunk 26 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.163987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134642 restraints weight = 15731.235| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.35 r_work: 0.3554 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2196 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= 0.132 Angle : 0.594 8.181 13966 Z= 0.306 Chirality : 0.042 0.226 1567 Planarity : 0.004 0.041 1766 Dihedral : 4.704 73.556 1406 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.28 % Allowed : 26.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.24), residues: 1277 helix: 1.72 (0.25), residues: 416 sheet: -0.64 (0.27), residues: 331 loop : -1.12 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 245 TYR 0.033 0.002 TYR S 235 PHE 0.020 0.001 PHE R 214 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00295 (10304) covalent geometry : angle 0.59368 (13956) SS BOND : bond 0.00231 ( 5) SS BOND : angle 1.19216 ( 10) hydrogen bonds : bond 0.03574 ( 490) hydrogen bonds : angle 4.75793 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3480.50 seconds wall clock time: 60 minutes 22.56 seconds (3622.56 seconds total)