Starting phenix.real_space_refine on Tue Aug 26 04:32:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p65_17461/08_2025/8p65_17461.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p65_17461/08_2025/8p65_17461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p65_17461/08_2025/8p65_17461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p65_17461/08_2025/8p65_17461.map" model { file = "/net/cci-nas-00/data/ceres_data/8p65_17461/08_2025/8p65_17461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p65_17461/08_2025/8p65_17461.cif" } resolution = 3.0 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 10 7.16 5 S 170 5.16 5 C 21620 2.51 5 N 5828 2.21 5 O 6192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 238 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33820 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3457 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain: "B" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3280 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain: "C" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3010 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 22, 'TRANS': 356} Chain: "D" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1918 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 22, 'TRANS': 218} Chain: "E" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1519 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 950 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 689 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain: "H" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 638 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "I" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 383 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "J" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 528 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "K" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "N" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3457 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain: "O" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3280 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain: "P" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3010 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 22, 'TRANS': 356} Chain: "Q" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1918 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 22, 'TRANS': 218} Chain: "R" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1519 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "S" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 950 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "T" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 689 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain: "U" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 638 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "V" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 383 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 528 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "X" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12759 SG CYS E 139 99.102 75.747 42.590 1.00200.54 S ATOM 12895 SG CYS E 158 98.194 79.176 41.727 1.00198.14 S ATOM 29536 SG CYS R 139 33.820 71.546 43.338 1.00199.37 S ATOM 29571 SG CYS R 144 37.782 68.383 41.283 1.00185.23 S ATOM 29685 SG CYS R 160 37.667 65.796 42.673 1.00217.56 S Time building chain proxies: 7.51, per 1000 atoms: 0.22 Number of scatterers: 33820 At special positions: 0 Unit cell: (131.58, 149.124, 173.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 10 26.01 S 170 16.00 O 6192 8.00 N 5828 7.00 C 21620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 160 " distance=2.03 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 30 " distance=2.08 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 54 " distance=2.03 Simple disulfide: pdb=" SG CYS U 24 " - pdb=" SG CYS U 68 " distance=2.02 Simple disulfide: pdb=" SG CYS U 40 " - pdb=" SG CYS U 54 " 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" ND1 HIS E 161 " pdb="FE2 FES E 201 " - pdb=" ND1 HIS E 141 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 139 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 158 " pdb=" FES R 201 " pdb="FE1 FES R 201 " - pdb=" NE2 HIS R 161 " pdb="FE2 FES R 201 " - pdb=" SG CYS R 144 " pdb="FE2 FES R 201 " - pdb=" SG CYS R 160 " pdb="FE1 FES R 201 " - pdb=" SG CYS R 139 " Number of angles added : 7 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7992 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 19 sheets defined 55.0% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 54 through 64 removed outlier: 4.402A pdb=" N PHE A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.527A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 119 Processing helix chain 'A' and resid 123 through 142 removed outlier: 3.603A pdb=" N ASP A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 190 Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 330 through 348 removed outlier: 3.984A pdb=" N VAL A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 369 removed outlier: 3.942A pdb=" N LEU A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 386 removed outlier: 3.565A pdb=" N GLU A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 403 through 415 Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.563A pdb=" N GLU B 58 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.749A pdb=" N VAL B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.717A pdb=" N LEU B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 141 Processing helix chain 'B' and resid 142 through 152 removed outlier: 3.548A pdb=" N ILE B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 168 removed outlier: 3.702A pdb=" N VAL B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 160 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 212 through 218 Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.745A pdb=" N ASN B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 301 removed outlier: 3.903A pdb=" N LYS B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 349 removed outlier: 3.637A pdb=" N VAL B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 374 removed outlier: 3.970A pdb=" N SER B 374 " --> pdb=" O MET B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 389 Processing helix chain 'B' and resid 394 through 404 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.511A pdb=" N VAL B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 19 removed outlier: 3.566A pdb=" N ALA C 17 " --> pdb=" O VAL C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 31 through 52 removed outlier: 4.259A pdb=" N SER C 35 " --> pdb=" O TRP C 31 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 75 through 104 removed outlier: 3.931A pdb=" N ILE C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 101 " --> pdb=" O HIS C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 109 through 133 removed outlier: 3.566A pdb=" N VAL C 132 " --> pdb=" O PHE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.550A pdb=" N ILE C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 156 through 166 Processing helix chain 'C' and resid 171 through 199 Proline residue: C 186 - end of helix Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 220 through 246 removed outlier: 3.720A pdb=" N THR C 225 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 227 " --> pdb=" O TYR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 286 through 300 removed outlier: 3.713A pdb=" N ILE C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 Proline residue: C 305 - end of helix removed outlier: 3.809A pdb=" N HIS C 308 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 317 removed outlier: 4.044A pdb=" N PHE C 317 " --> pdb=" O SER C 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 314 through 317' Processing helix chain 'C' and resid 318 through 340 removed outlier: 3.552A pdb=" N LEU C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 364 removed outlier: 3.971A pdb=" N THR C 349 " --> pdb=" O HIS C 345 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 350 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 362 " --> pdb=" O TYR C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 377 Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.507A pdb=" N GLN D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 40 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 123 through 133 Processing helix chain 'D' and resid 178 through 195 removed outlier: 3.596A pdb=" N ALA D 183 " --> pdb=" O MET D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 232 Proline residue: D 217 - end of helix removed outlier: 4.529A pdb=" N VAL D 229 " --> pdb=" O HIS D 225 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 5 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 28 through 62 removed outlier: 4.074A pdb=" N MET E 62 " --> pdb=" O PHE E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.511A pdb=" N LYS E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.867A pdb=" N ILE E 106 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLN E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA E 110 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL E 112 " --> pdb=" O GLN E 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 112' Processing helix chain 'E' and resid 113 through 117 removed outlier: 3.547A pdb=" N GLN E 116 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU E 117 " --> pdb=" O VAL E 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 113 through 117' Processing helix chain 'F' and resid 14 through 26 Processing helix chain 'F' and resid 33 through 37 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'F' and resid 52 through 72 Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.950A pdb=" N TRP F 81 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 109 removed outlier: 3.577A pdb=" N GLU F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 24 removed outlier: 3.868A pdb=" N GLN G 24 " --> pdb=" O PRO G 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 21 through 24' Processing helix chain 'G' and resid 29 through 72 removed outlier: 4.087A pdb=" N ILE G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Proline residue: G 36 - end of helix removed outlier: 4.293A pdb=" N LEU G 47 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ARG G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) Proline residue: G 51 - end of helix removed outlier: 3.682A pdb=" N PHE G 56 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN G 65 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 22 removed outlier: 3.692A pdb=" N THR H 19 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 26 Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.746A pdb=" N ARG H 34 " --> pdb=" O CYS H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 72 removed outlier: 3.979A pdb=" N LYS H 72 " --> pdb=" O CYS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'J' and resid 5 through 14 removed outlier: 3.713A pdb=" N ARG J 9 " --> pdb=" O THR J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 48 removed outlier: 3.504A pdb=" N GLN J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE J 43 " --> pdb=" O GLY J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 57 removed outlier: 3.553A pdb=" N ILE J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 60 No H-bonds generated for 'chain 'J' and resid 58 through 60' Processing helix chain 'K' and resid 7 through 17 Processing helix chain 'K' and resid 17 through 36 removed outlier: 4.243A pdb=" N ALA K 26 " --> pdb=" O SER K 22 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL K 27 " --> pdb=" O LEU K 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY K 28 " --> pdb=" O TRP K 24 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU K 32 " --> pdb=" O GLY K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 43 Processing helix chain 'N' and resid 3 through 10 removed outlier: 3.872A pdb=" N GLN N 9 " --> pdb=" O ALA N 5 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER N 10 " --> pdb=" O GLN N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 48 Processing helix chain 'N' and resid 54 through 64 removed outlier: 4.351A pdb=" N PHE N 64 " --> pdb=" O GLU N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 83 removed outlier: 3.514A pdb=" N VAL N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 119 Processing helix chain 'N' and resid 123 through 142 removed outlier: 3.644A pdb=" N ASP N 132 " --> pdb=" O GLU N 128 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL N 133 " --> pdb=" O LYS N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 158 Processing helix chain 'N' and resid 161 through 165 Processing helix chain 'N' and resid 170 through 177 Processing helix chain 'N' and resid 178 through 190 Processing helix chain 'N' and resid 191 through 193 No H-bonds generated for 'chain 'N' and resid 191 through 193' Processing helix chain 'N' and resid 204 through 216 Processing helix chain 'N' and resid 217 through 219 No H-bonds generated for 'chain 'N' and resid 217 through 219' Processing helix chain 'N' and resid 265 through 278 removed outlier: 4.486A pdb=" N ALA N 269 " --> pdb=" O PRO N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 290 removed outlier: 3.575A pdb=" N LEU N 290 " --> pdb=" O GLY N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 301 Processing helix chain 'N' and resid 330 through 348 removed outlier: 4.677A pdb=" N VAL N 337 " --> pdb=" O ASP N 333 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 369 removed outlier: 3.566A pdb=" N VAL N 354 " --> pdb=" O THR N 350 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU N 369 " --> pdb=" O LEU N 365 " (cutoff:3.500A) Processing helix chain 'N' and resid 372 through 386 removed outlier: 3.552A pdb=" N LEU N 384 " --> pdb=" O GLY N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 391 through 401 Processing helix chain 'N' and resid 403 through 415 Processing helix chain 'N' and resid 433 through 439 Processing helix chain 'N' and resid 440 through 442 No H-bonds generated for 'chain 'N' and resid 440 through 442' Processing helix chain 'O' and resid 54 through 58 removed outlier: 3.638A pdb=" N GLU O 58 " --> pdb=" O SER O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 72 Processing helix chain 'O' and resid 81 through 92 removed outlier: 3.813A pdb=" N VAL O 92 " --> pdb=" O GLY O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 129 removed outlier: 3.670A pdb=" N LEU O 119 " --> pdb=" O ASP O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 140 Processing helix chain 'O' and resid 140 through 152 removed outlier: 3.724A pdb=" N LEU O 144 " --> pdb=" O LEU O 140 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG O 145 " --> pdb=" O GLN O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 168 removed outlier: 3.955A pdb=" N HIS O 158 " --> pdb=" O ASN O 154 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL O 159 " --> pdb=" O PRO O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 174 Processing helix chain 'O' and resid 187 through 199 Processing helix chain 'O' and resid 200 through 202 No H-bonds generated for 'chain 'O' and resid 200 through 202' Processing helix chain 'O' and resid 212 through 220 Processing helix chain 'O' and resid 266 through 279 removed outlier: 3.769A pdb=" N ASN O 270 " --> pdb=" O SER O 266 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 301 removed outlier: 3.879A pdb=" N LYS O 301 " --> pdb=" O GLN O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 332 through 349 removed outlier: 3.671A pdb=" N VAL O 336 " --> pdb=" O SER O 332 " (cutoff:3.500A) Processing helix chain 'O' and resid 353 through 372 Processing helix chain 'O' and resid 374 through 389 Processing helix chain 'O' and resid 394 through 404 Processing helix chain 'O' and resid 406 through 420 Processing helix chain 'P' and resid 11 through 20 removed outlier: 4.380A pdb=" N ALA P 17 " --> pdb=" O ILE P 13 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE P 18 " --> pdb=" O VAL P 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE P 19 " --> pdb=" O ASN P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 31 removed outlier: 3.501A pdb=" N TRP P 31 " --> pdb=" O SER P 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 28 through 31' Processing helix chain 'P' and resid 32 through 52 removed outlier: 3.505A pdb=" N PHE P 50 " --> pdb=" O LEU P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 61 Processing helix chain 'P' and resid 62 through 72 Processing helix chain 'P' and resid 75 through 104 removed outlier: 3.882A pdb=" N ILE P 79 " --> pdb=" O TYR P 75 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER P 88 " --> pdb=" O ALA P 84 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY P 101 " --> pdb=" O HIS P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 108 Processing helix chain 'P' and resid 109 through 132 removed outlier: 3.695A pdb=" N VAL P 132 " --> pdb=" O PHE P 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 138 through 148 removed outlier: 3.508A pdb=" N ILE P 146 " --> pdb=" O GLY P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 153 Processing helix chain 'P' and resid 156 through 166 Processing helix chain 'P' and resid 171 through 202 Proline residue: P 186 - end of helix removed outlier: 3.548A pdb=" N ALA P 191 " --> pdb=" O PHE P 187 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU P 200 " --> pdb=" O HIS P 196 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU P 202 " --> pdb=" O LEU P 198 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 215 No H-bonds generated for 'chain 'P' and resid 213 through 215' Processing helix chain 'P' and resid 224 through 246 Processing helix chain 'P' and resid 252 through 257 Processing helix chain 'P' and resid 274 through 284 removed outlier: 3.917A pdb=" N ILE P 280 " --> pdb=" O PHE P 276 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE P 284 " --> pdb=" O ILE P 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 286 through 300 removed outlier: 3.634A pdb=" N ILE P 298 " --> pdb=" O LEU P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 308 Proline residue: P 305 - end of helix removed outlier: 3.800A pdb=" N HIS P 308 " --> pdb=" O PRO P 305 " (cutoff:3.500A) Processing helix chain 'P' and resid 314 through 317 removed outlier: 4.315A pdb=" N PHE P 317 " --> pdb=" O SER P 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 314 through 317' Processing helix chain 'P' and resid 318 through 340 removed outlier: 3.536A pdb=" N LEU P 324 " --> pdb=" O LEU P 320 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY P 340 " --> pdb=" O THR P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 344 through 364 removed outlier: 3.698A pdb=" N THR P 349 " --> pdb=" O HIS P 345 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE P 362 " --> pdb=" O TYR P 358 " (cutoff:3.500A) Processing helix chain 'P' and resid 364 through 377 Processing helix chain 'Q' and resid 22 through 36 Processing helix chain 'Q' and resid 37 through 40 Processing helix chain 'Q' and resid 57 through 67 Processing helix chain 'Q' and resid 97 through 105 Processing helix chain 'Q' and resid 123 through 133 Processing helix chain 'Q' and resid 178 through 195 Processing helix chain 'Q' and resid 197 through 232 removed outlier: 3.532A pdb=" N LYS Q 207 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU Q 214 " --> pdb=" O LEU Q 210 " (cutoff:3.500A) Proline residue: Q 217 - end of helix removed outlier: 4.547A pdb=" N VAL Q 229 " --> pdb=" O HIS Q 225 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU Q 230 " --> pdb=" O LYS Q 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 1 through 5 Processing helix chain 'R' and resid 16 through 20 removed outlier: 4.032A pdb=" N ASP R 20 " --> pdb=" O GLU R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 62 removed outlier: 3.569A pdb=" N SER R 36 " --> pdb=" O ARG R 32 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET R 62 " --> pdb=" O PHE R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 71 removed outlier: 4.150A pdb=" N MET R 71 " --> pdb=" O ASP R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 112 removed outlier: 3.549A pdb=" N ILE R 106 " --> pdb=" O THR R 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLN R 108 " --> pdb=" O LYS R 104 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA R 110 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL R 112 " --> pdb=" O GLN R 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 26 removed outlier: 4.234A pdb=" N ARG S 18 " --> pdb=" O LEU S 14 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS S 19 " --> pdb=" O GLU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 37 Processing helix chain 'S' and resid 43 through 50 Processing helix chain 'S' and resid 52 through 72 Processing helix chain 'S' and resid 77 through 81 removed outlier: 3.946A pdb=" N TRP S 81 " --> pdb=" O LYS S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 110 removed outlier: 3.572A pdb=" N GLU S 97 " --> pdb=" O PRO S 93 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS S 110 " --> pdb=" O GLU S 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 24 removed outlier: 3.871A pdb=" N GLN T 24 " --> pdb=" O PRO T 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 21 through 24' Processing helix chain 'T' and resid 29 through 72 removed outlier: 3.978A pdb=" N ILE T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Proline residue: T 36 - end of helix removed outlier: 4.237A pdb=" N LEU T 47 " --> pdb=" O ARG T 43 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ARG T 48 " --> pdb=" O ALA T 44 " (cutoff:3.500A) Proline residue: T 51 - end of helix removed outlier: 3.673A pdb=" N PHE T 56 " --> pdb=" O PRO T 52 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN T 65 " --> pdb=" O THR T 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 23 Processing helix chain 'U' and resid 27 through 46 Processing helix chain 'U' and resid 55 through 72 removed outlier: 3.526A pdb=" N ALA U 70 " --> pdb=" O ASP U 66 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS U 72 " --> pdb=" O CYS U 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 34 removed outlier: 3.555A pdb=" N ALA V 33 " --> pdb=" O LEU V 29 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL V 34 " --> pdb=" O VAL V 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 29 through 34' Processing helix chain 'W' and resid 5 through 14 removed outlier: 3.587A pdb=" N ARG W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU W 14 " --> pdb=" O LEU W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 48 removed outlier: 3.514A pdb=" N LEU W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN W 38 " --> pdb=" O ARG W 34 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE W 43 " --> pdb=" O GLY W 39 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR W 44 " --> pdb=" O ALA W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 60 removed outlier: 3.764A pdb=" N LYS W 59 " --> pdb=" O ILE W 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 37 removed outlier: 3.502A pdb=" N TRP X 17 " --> pdb=" O LEU X 13 " (cutoff:3.500A) Proline residue: X 19 - end of helix removed outlier: 3.653A pdb=" N ALA X 26 " --> pdb=" O SER X 22 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL X 27 " --> pdb=" O LEU X 23 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 304 through 313 removed outlier: 3.577A pdb=" N VAL G 14 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.874A pdb=" N GLU B 25 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 34 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLY B 208 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA B 36 " --> pdb=" O GLY B 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 243 through 245 removed outlier: 3.570A pdb=" N GLY B 320 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 71 Processing sheet with id=AA7, first strand: chain 'D' and resid 148 through 149 Processing sheet with id=AA8, first strand: chain 'E' and resid 75 through 77 removed outlier: 3.783A pdb=" N ILE E 76 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL E 193 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE E 194 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU E 186 " --> pdb=" O ILE E 194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 87 through 91 removed outlier: 3.988A pdb=" N MET E 87 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE E 89 " --> pdb=" O LEU E 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 156 through 157 Processing sheet with id=AB2, first strand: chain 'I' and resid 14 through 16 removed outlier: 6.216A pdb=" N VAL O 34 " --> pdb=" O LEU O 206 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLY O 208 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA O 36 " --> pdb=" O GLY O 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 15 through 18 removed outlier: 3.570A pdb=" N ARG N 24 " --> pdb=" O MET N 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 304 through 313 removed outlier: 3.519A pdb=" N VAL T 14 " --> pdb=" O ARG N 244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 243 through 245 Processing sheet with id=AB6, first strand: chain 'P' and resid 22 through 24 Processing sheet with id=AB7, first strand: chain 'Q' and resid 69 through 71 Processing sheet with id=AB8, first strand: chain 'R' and resid 75 through 77 removed outlier: 3.522A pdb=" N VAL R 193 " --> pdb=" O ILE R 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 88 through 91 removed outlier: 3.560A pdb=" N PHE R 89 " --> pdb=" O LEU R 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 156 through 157 removed outlier: 3.953A pdb=" N TYR R 156 " --> pdb=" O TYR R 165 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS R 164 " --> pdb=" O ARG R 172 " (cutoff:3.500A) 1722 hydrogen bonds defined for protein. 4935 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: 5.87 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 14297 1.40 - 1.60: 20081 1.60 - 1.80: 213 1.80 - 2.00: 51 2.00 - 2.21: 32 Bond restraints: 34674 Sorted by residual: bond pdb=" N THR N 161 " pdb=" CA THR N 161 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.73e+01 bond pdb=" C PRO B 18 " pdb=" N PRO B 19 " ideal model delta sigma weight residual 1.334 1.361 -0.027 8.40e-03 1.42e+04 1.03e+01 bond pdb=" N GLU U 6 " pdb=" CA GLU U 6 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.38e+00 bond pdb=" N LYS U 4 " pdb=" CA LYS U 4 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.36e-02 5.41e+03 9.31e+00 bond pdb=" N THR A 161 " pdb=" CA THR A 161 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.18e-02 7.18e+03 8.71e+00 ... (remaining 34669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 46493 2.40 - 4.79: 572 4.79 - 7.19: 70 7.19 - 9.58: 14 9.58 - 11.98: 7 Bond angle restraints: 47156 Sorted by residual: angle pdb=" N GLU H 25 " pdb=" CA GLU H 25 " pdb=" C GLU H 25 " ideal model delta sigma weight residual 114.12 102.14 11.98 1.39e+00 5.18e-01 7.43e+01 angle pdb=" C CYS R 158 " pdb=" CA CYS R 158 " pdb=" CB CYS R 158 " ideal model delta sigma weight residual 110.17 117.23 -7.06 9.90e-01 1.02e+00 5.08e+01 angle pdb=" N ALA K 21 " pdb=" CA ALA K 21 " pdb=" C ALA K 21 " ideal model delta sigma weight residual 111.82 105.23 6.59 1.16e+00 7.43e-01 3.23e+01 angle pdb=" C LYS U 4 " pdb=" N GLU U 5 " pdb=" CA GLU U 5 " ideal model delta sigma weight residual 122.53 114.96 7.57 1.61e+00 3.86e-01 2.21e+01 angle pdb=" C LYS U 4 " pdb=" CA LYS U 4 " pdb=" CB LYS U 4 " ideal model delta sigma weight residual 114.52 106.48 8.04 1.81e+00 3.05e-01 1.98e+01 ... (remaining 47151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17451 17.93 - 35.87: 2319 35.87 - 53.80: 670 53.80 - 71.73: 103 71.73 - 89.67: 62 Dihedral angle restraints: 20605 sinusoidal: 8187 harmonic: 12418 Sorted by residual: dihedral pdb=" CA ASP A 281 " pdb=" C ASP A 281 " pdb=" N CYS A 282 " pdb=" CA CYS A 282 " ideal model delta harmonic sigma weight residual 180.00 156.25 23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA LYS O 3 " pdb=" C LYS O 3 " pdb=" N VAL O 4 " pdb=" CA VAL O 4 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA PRO I 35 " pdb=" C PRO I 35 " pdb=" N ALA I 36 " pdb=" CA ALA I 36 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 20602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4289 0.054 - 0.108: 785 0.108 - 0.162: 89 0.162 - 0.216: 4 0.216 - 0.270: 1 Chirality restraints: 5168 Sorted by residual: chirality pdb=" CA VAL O 8 " pdb=" N VAL O 8 " pdb=" C VAL O 8 " pdb=" CB VAL O 8 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA SER O 201 " pdb=" N SER O 201 " pdb=" C SER O 201 " pdb=" CB SER O 201 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PRO J 4 " pdb=" N PRO J 4 " pdb=" C PRO J 4 " pdb=" CB PRO J 4 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 5165 not shown) Planarity restraints: 6040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 301 " -0.016 2.00e-02 2.50e+03 4.34e-02 4.25e+01 pdb=" C2C HEC D 301 " 0.119 2.00e-02 2.50e+03 pdb=" C3C HEC D 301 " -0.020 2.00e-02 2.50e+03 pdb=" C4C HEC D 301 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC D 301 " -0.019 2.00e-02 2.50e+03 pdb=" CHC HEC D 301 " -0.018 2.00e-02 2.50e+03 pdb=" CHD HEC D 301 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC D 301 " -0.038 2.00e-02 2.50e+03 pdb=" NC HEC D 301 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q 301 " 0.016 2.00e-02 2.50e+03 4.26e-02 4.08e+01 pdb=" C2C HEC Q 301 " -0.117 2.00e-02 2.50e+03 pdb=" C3C HEC Q 301 " 0.020 2.00e-02 2.50e+03 pdb=" C4C HEC Q 301 " 0.006 2.00e-02 2.50e+03 pdb=" CAC HEC Q 301 " 0.019 2.00e-02 2.50e+03 pdb=" CHC HEC Q 301 " 0.019 2.00e-02 2.50e+03 pdb=" CHD HEC Q 301 " -0.004 2.00e-02 2.50e+03 pdb=" CMC HEC Q 301 " 0.036 2.00e-02 2.50e+03 pdb=" NC HEC Q 301 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA J 3 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO J 4 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO J 4 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO J 4 " 0.056 5.00e-02 4.00e+02 ... (remaining 6037 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 500 2.62 - 3.19: 30201 3.19 - 3.76: 54781 3.76 - 4.33: 75675 4.33 - 4.90: 124951 Nonbonded interactions: 286108 Sorted by model distance: nonbonded pdb=" OG SER H 48 " pdb=" OE1 GLN H 49 " model vdw 2.056 3.040 nonbonded pdb=" O SER S 11 " pdb=" OG SER S 11 " model vdw 2.191 3.040 nonbonded pdb=" O ILE C 13 " pdb=" ND2 ASN C 16 " model vdw 2.201 3.120 nonbonded pdb=" O ALA C 143 " pdb=" OG1 THR C 147 " model vdw 2.204 3.040 nonbonded pdb=" O PRO C 24 " pdb=" OH TYR C 224 " model vdw 2.204 3.040 ... (remaining 286103 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'S' } ncs_group { reference = chain 'G' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'W' } ncs_group { reference = chain 'K' selection = chain 'X' } 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 31.250 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 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 : 0.005 0.502 34693 Z= 0.175 Angle : 0.635 28.426 47173 Z= 0.321 Chirality : 0.041 0.270 5168 Planarity : 0.004 0.104 6040 Dihedral : 17.916 89.669 12598 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.24 % Favored : 94.38 % Rotamer: Outliers : 6.10 % Allowed : 27.16 % Favored : 66.74 % 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: -0.20 (0.13), residues: 4234 helix: 0.72 (0.12), residues: 1937 sheet: -0.15 (0.28), residues: 386 loop : -0.98 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 20 TYR 0.018 0.001 TYR P 224 PHE 0.023 0.001 PHE A 336 TRP 0.029 0.001 TRP A 443 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00360 (34674) covalent geometry : angle 0.61864 (47156) SS BOND : bond 0.02169 ( 5) SS BOND : angle 2.77360 ( 10) hydrogen bonds : bond 0.25685 ( 1722) hydrogen bonds : angle 7.98134 ( 4935) metal coordination : bond 0.00623 ( 8) metal coordination : angle 11.33553 ( 7) Misc. bond : bond 0.23067 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 720 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.8779 (t) cc_final: 0.8552 (p) REVERT: A 145 MET cc_start: 0.7244 (ttm) cc_final: 0.6929 (ttm) REVERT: A 156 THR cc_start: 0.7010 (p) cc_final: 0.6565 (t) REVERT: A 294 LEU cc_start: 0.7825 (tp) cc_final: 0.7620 (tp) REVERT: A 307 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.5998 (p90) REVERT: A 308 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.6342 (mp10) REVERT: B 110 GLU cc_start: 0.6706 (tt0) cc_final: 0.6463 (tt0) REVERT: B 223 PHE cc_start: 0.6040 (OUTLIER) cc_final: 0.5702 (p90) REVERT: B 381 GLU cc_start: 0.7817 (tp30) cc_final: 0.7252 (tp30) REVERT: B 392 TYR cc_start: 0.4853 (t80) cc_final: 0.4165 (t80) REVERT: C 8 HIS cc_start: 0.0456 (OUTLIER) cc_final: 0.0029 (t70) REVERT: C 107 TYR cc_start: 0.6954 (p90) cc_final: 0.6515 (p90) REVERT: C 161 VAL cc_start: 0.8155 (t) cc_final: 0.7776 (m) REVERT: C 211 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7327 (mp) REVERT: C 216 ASP cc_start: 0.7775 (t70) cc_final: 0.6964 (m-30) REVERT: C 312 GLN cc_start: 0.7190 (mt0) cc_final: 0.6848 (mt0) REVERT: D 200 HIS cc_start: 0.6286 (t-90) cc_final: 0.5892 (t70) REVERT: E 37 TYR cc_start: 0.7699 (m-10) cc_final: 0.7251 (m-10) REVERT: E 62 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6921 (mtm) REVERT: E 140 THR cc_start: 0.6633 (OUTLIER) cc_final: 0.5009 (p) REVERT: E 157 TYR cc_start: 0.3704 (t80) cc_final: 0.3443 (t80) REVERT: E 192 MET cc_start: 0.5330 (tpp) cc_final: 0.5119 (mmp) REVERT: H 32 LYS cc_start: 0.8052 (tppp) cc_final: 0.7747 (tppp) REVERT: J 1 MET cc_start: 0.1513 (ptt) cc_final: -0.0367 (ptp) REVERT: N 48 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7411 (pt0) REVERT: N 146 ARG cc_start: 0.6926 (mtp-110) cc_final: 0.6624 (tpt90) REVERT: N 186 LEU cc_start: 0.8913 (mt) cc_final: 0.8689 (mm) REVERT: N 329 MET cc_start: 0.6904 (tpp) cc_final: 0.6327 (mmt) REVERT: N 415 PHE cc_start: 0.7008 (m-10) cc_final: 0.6670 (m-10) REVERT: O 85 ILE cc_start: 0.7672 (mt) cc_final: 0.7337 (mm) REVERT: O 200 THR cc_start: 0.7005 (p) cc_final: 0.6790 (p) REVERT: O 278 VAL cc_start: 0.8036 (t) cc_final: 0.7790 (t) REVERT: P 35 SER cc_start: 0.7336 (t) cc_final: 0.6811 (m) REVERT: P 36 LEU cc_start: 0.7385 (mt) cc_final: 0.7016 (mp) REVERT: P 57 SER cc_start: 0.7838 (OUTLIER) cc_final: 0.7575 (m) REVERT: P 82 MET cc_start: 0.7875 (mtm) cc_final: 0.7352 (mtp) REVERT: P 163 TRP cc_start: 0.7935 (t60) cc_final: 0.7330 (t60) REVERT: P 236 ILE cc_start: 0.7849 (mm) cc_final: 0.7615 (mm) REVERT: Q 33 TYR cc_start: 0.6675 (t80) cc_final: 0.6419 (t80) REVERT: Q 115 TYR cc_start: 0.7824 (m-80) cc_final: 0.7426 (m-80) REVERT: R 97 PHE cc_start: 0.7236 (m-10) cc_final: 0.6995 (m-80) REVERT: R 181 GLU cc_start: 0.4347 (tm-30) cc_final: 0.4124 (tm-30) REVERT: S 45 LYS cc_start: 0.7259 (tptp) cc_final: 0.6973 (mtpm) REVERT: T 1 MET cc_start: -0.0453 (mpt) cc_final: -0.1577 (pmm) REVERT: T 4 GLN cc_start: 0.6155 (pm20) cc_final: 0.5664 (pp30) REVERT: T 47 LEU cc_start: 0.6758 (mm) cc_final: 0.6377 (mt) REVERT: T 54 VAL cc_start: 0.7651 (OUTLIER) cc_final: 0.7408 (p) REVERT: T 74 ASN cc_start: 0.8424 (p0) cc_final: 0.8177 (p0) REVERT: U 29 LYS cc_start: 0.8762 (tptm) cc_final: 0.8517 (tppp) REVERT: W 7 THR cc_start: 0.7520 (OUTLIER) cc_final: 0.7003 (m) REVERT: W 11 TYR cc_start: 0.7183 (t80) cc_final: 0.6802 (t80) REVERT: W 57 LYS cc_start: 0.7717 (mtpp) cc_final: 0.7428 (ttmm) REVERT: X 39 ARG cc_start: 0.5667 (pmt170) cc_final: 0.4848 (mpp-170) REVERT: X 48 ILE cc_start: 0.4677 (OUTLIER) cc_final: 0.4387 (mt) outliers start: 219 outliers final: 58 residues processed: 896 average time/residue: 0.4791 time to fit residues: 536.4716 Evaluate side-chains 519 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 450 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain K residue 38 TRP Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 313 CYS Chi-restraints excluded: chain N residue 446 PHE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 335 ASP Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 213 SER Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 68 CYS Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 240 HIS B 297 GLN D 31 GLN D 35 GLN D 71 GLN D 166 ASN G 7 HIS G 80 ASN J 48 ASN N 240 GLN N 430 GLN O 20 HIS O 174 ASN O 284 HIS P 74 ASN Q 31 GLN Q 71 GLN W 48 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.125405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.097977 restraints weight = 62543.428| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.84 r_work: 0.3294 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.421 34693 Z= 0.216 Angle : 0.796 30.164 47173 Z= 0.393 Chirality : 0.047 0.219 5168 Planarity : 0.006 0.104 6040 Dihedral : 7.798 87.284 4829 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.96 % Favored : 94.76 % Rotamer: Outliers : 6.91 % Allowed : 26.55 % Favored : 66.55 % 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: -0.16 (0.13), residues: 4234 helix: 0.73 (0.11), residues: 2065 sheet: -0.12 (0.27), residues: 392 loop : -1.04 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 39 TYR 0.033 0.002 TYR A 434 PHE 0.023 0.002 PHE B 378 TRP 0.023 0.002 TRP P 163 HIS 0.014 0.002 HIS N 61 Details of bonding type rmsd covalent geometry : bond 0.00486 (34674) covalent geometry : angle 0.77567 (47156) SS BOND : bond 0.00573 ( 5) SS BOND : angle 1.67268 ( 10) hydrogen bonds : bond 0.05000 ( 1722) hydrogen bonds : angle 5.19965 ( 4935) metal coordination : bond 0.01436 ( 8) metal coordination : angle 14.75234 ( 7) Misc. bond : bond 0.24230 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 445 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: A 116 ILE cc_start: 0.7665 (mt) cc_final: 0.7448 (mp) REVERT: A 339 GLN cc_start: 0.8260 (mt0) cc_final: 0.8021 (mt0) REVERT: A 342 TRP cc_start: 0.7967 (m-10) cc_final: 0.7425 (m-10) REVERT: B 110 GLU cc_start: 0.7892 (tt0) cc_final: 0.7552 (tt0) REVERT: B 223 PHE cc_start: 0.5873 (OUTLIER) cc_final: 0.5538 (p90) REVERT: B 354 ASN cc_start: 0.8448 (t0) cc_final: 0.8246 (t0) REVERT: B 376 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7360 (tm-30) REVERT: B 385 GLN cc_start: 0.7087 (mt0) cc_final: 0.6733 (tt0) REVERT: B 407 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.6770 (t0) REVERT: C 155 TYR cc_start: 0.7276 (t80) cc_final: 0.6649 (t80) REVERT: C 211 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7487 (mm) REVERT: C 373 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7517 (pt0) REVERT: D 82 MET cc_start: 0.8253 (mmm) cc_final: 0.7928 (mmp) REVERT: D 166 ASN cc_start: 0.8127 (m-40) cc_final: 0.7830 (m-40) REVERT: E 118 ARG cc_start: 0.1148 (OUTLIER) cc_final: -0.3511 (ttt180) REVERT: E 192 MET cc_start: 0.5343 (tpp) cc_final: 0.5114 (mmt) REVERT: F 97 GLU cc_start: 0.7156 (tp30) cc_final: 0.6836 (tp30) REVERT: F 100 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7286 (ttp80) REVERT: H 69 VAL cc_start: 0.8157 (t) cc_final: 0.7918 (t) REVERT: I 2 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8148 (mp) REVERT: J 45 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: K 22 SER cc_start: 0.4719 (OUTLIER) cc_final: 0.4224 (p) REVERT: N 149 VAL cc_start: 0.7612 (t) cc_final: 0.7274 (p) REVERT: N 329 MET cc_start: 0.8149 (tpp) cc_final: 0.7744 (tpp) REVERT: N 383 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8147 (mm) REVERT: N 415 PHE cc_start: 0.7783 (m-10) cc_final: 0.7506 (m-10) REVERT: O 96 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7692 (tt) REVERT: O 105 MET cc_start: 0.7864 (ttt) cc_final: 0.7595 (ttm) REVERT: O 146 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7961 (tt) REVERT: O 200 THR cc_start: 0.8335 (p) cc_final: 0.8040 (p) REVERT: O 278 VAL cc_start: 0.7905 (t) cc_final: 0.7576 (t) REVERT: O 379 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6205 (tp) REVERT: O 438 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: P 75 TYR cc_start: 0.7719 (m-80) cc_final: 0.7324 (m-80) REVERT: P 82 MET cc_start: 0.8288 (mtm) cc_final: 0.7725 (mtp) REVERT: P 102 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8797 (mm) REVERT: P 129 MET cc_start: 0.8224 (mtm) cc_final: 0.8020 (mtm) REVERT: P 133 LEU cc_start: 0.9188 (mt) cc_final: 0.8934 (mp) REVERT: P 198 LEU cc_start: 0.8676 (tp) cc_final: 0.8453 (tt) REVERT: P 199 PHE cc_start: 0.8083 (m-80) cc_final: 0.7783 (m-80) REVERT: P 268 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.7941 (pp) REVERT: Q 115 TYR cc_start: 0.8439 (m-80) cc_final: 0.8117 (m-80) REVERT: Q 160 MET cc_start: 0.8354 (ttp) cc_final: 0.7829 (ttp) REVERT: Q 211 MET cc_start: 0.8245 (mmm) cc_final: 0.8026 (mmm) REVERT: R 87 MET cc_start: 0.7246 (tpp) cc_final: 0.6964 (tpp) REVERT: R 136 ILE cc_start: 0.8432 (pp) cc_final: 0.8200 (mm) REVERT: S 22 TYR cc_start: 0.8349 (t80) cc_final: 0.8076 (t80) REVERT: S 33 MET cc_start: 0.8277 (mpp) cc_final: 0.8026 (mpp) REVERT: S 45 LYS cc_start: 0.7619 (tptp) cc_final: 0.7283 (mtpm) REVERT: T 47 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7721 (mt) REVERT: T 74 ASN cc_start: 0.8523 (p0) cc_final: 0.8278 (p0) REVERT: U 13 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6755 (tm) REVERT: U 23 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8580 (tp40) REVERT: U 53 ASP cc_start: 0.8911 (p0) cc_final: 0.8492 (p0) REVERT: V 16 SER cc_start: 0.6849 (m) cc_final: 0.6610 (t) REVERT: W 7 THR cc_start: 0.7045 (OUTLIER) cc_final: 0.6808 (m) REVERT: W 18 THR cc_start: 0.8153 (t) cc_final: 0.7697 (m) REVERT: X 39 ARG cc_start: 0.5953 (pmt170) cc_final: 0.4823 (mpp-170) outliers start: 248 outliers final: 76 residues processed: 639 average time/residue: 0.4669 time to fit residues: 374.4674 Evaluate side-chains 451 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 356 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 38 TRP Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 240 GLN Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 376 CYS Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain N residue 446 PHE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 146 ILE Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 326 THR Chi-restraints excluded: chain O residue 379 LEU Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 172 LYS Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 284 ILE Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain R residue 89 PHE Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 15 ILE Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 68 CYS Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 361 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 314 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 326 optimal weight: 0.0060 chunk 59 optimal weight: 0.3980 chunk 308 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN B 174 ASN B 240 HIS B 247 GLN B 343 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS E 121 GLN G 80 ASN I 31 GLN K 16 ASN N 430 GLN O 284 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.125849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.097916 restraints weight = 62262.540| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.57 r_work: 0.3320 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.317 34693 Z= 0.140 Angle : 0.646 27.474 47173 Z= 0.313 Chirality : 0.042 0.211 5168 Planarity : 0.005 0.104 6040 Dihedral : 7.098 89.273 4769 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.68 % Favored : 95.04 % Rotamer: Outliers : 5.52 % Allowed : 27.21 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.16 (0.13), residues: 4234 helix: 1.11 (0.11), residues: 2039 sheet: -0.04 (0.27), residues: 377 loop : -0.99 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 34 TYR 0.024 0.001 TYR A 434 PHE 0.021 0.001 PHE A 324 TRP 0.026 0.001 TRP K 17 HIS 0.007 0.001 HIS O 240 Details of bonding type rmsd covalent geometry : bond 0.00316 (34674) covalent geometry : angle 0.62654 (47156) SS BOND : bond 0.00673 ( 5) SS BOND : angle 1.28762 ( 10) hydrogen bonds : bond 0.04600 ( 1722) hydrogen bonds : angle 4.83683 ( 4935) metal coordination : bond 0.00851 ( 8) metal coordination : angle 12.86707 ( 7) Misc. bond : bond 0.16818 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 378 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7549 (mttm) REVERT: A 136 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7756 (tp-100) REVERT: A 320 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7872 (tp) REVERT: A 342 TRP cc_start: 0.8049 (m-10) cc_final: 0.7465 (m-10) REVERT: B 110 GLU cc_start: 0.7993 (tt0) cc_final: 0.7659 (tt0) REVERT: B 140 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8215 (tt) REVERT: B 354 ASN cc_start: 0.8530 (t0) cc_final: 0.8266 (t0) REVERT: B 376 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7507 (tm-30) REVERT: B 407 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.6891 (t0) REVERT: B 424 MET cc_start: 0.7945 (tpp) cc_final: 0.7547 (ttt) REVERT: C 57 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8300 (m) REVERT: C 110 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8510 (mm) REVERT: C 155 TYR cc_start: 0.7373 (t80) cc_final: 0.6765 (t80) REVERT: C 211 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7779 (mm) REVERT: C 316 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6961 (mtm) REVERT: C 373 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: D 17 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8551 (tp) REVERT: D 82 MET cc_start: 0.8404 (mmm) cc_final: 0.7971 (mmp) REVERT: E 118 ARG cc_start: 0.1320 (OUTLIER) cc_final: -0.3487 (ttt180) REVERT: E 192 MET cc_start: 0.5602 (tpp) cc_final: 0.5274 (mmt) REVERT: F 1 MET cc_start: 0.3093 (ptm) cc_final: 0.2821 (pmt) REVERT: F 100 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7164 (ttp-110) REVERT: H 32 LYS cc_start: 0.8800 (tppp) cc_final: 0.8494 (tppp) REVERT: H 53 ASP cc_start: 0.8457 (p0) cc_final: 0.8063 (p0) REVERT: I 2 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7950 (mt) REVERT: J 45 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: N 307 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6755 (t80) REVERT: N 415 PHE cc_start: 0.7981 (m-10) cc_final: 0.7692 (m-10) REVERT: O 96 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7994 (tt) REVERT: O 105 MET cc_start: 0.8163 (ttt) cc_final: 0.7936 (ttm) REVERT: O 200 THR cc_start: 0.8501 (p) cc_final: 0.8199 (p) REVERT: O 278 VAL cc_start: 0.8474 (t) cc_final: 0.8103 (t) REVERT: P 75 TYR cc_start: 0.7719 (m-80) cc_final: 0.7426 (m-80) REVERT: P 164 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7634 (mp) REVERT: P 268 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7728 (pp) REVERT: P 345 HIS cc_start: 0.6374 (OUTLIER) cc_final: 0.4919 (p-80) REVERT: Q 115 TYR cc_start: 0.8401 (m-80) cc_final: 0.8107 (m-80) REVERT: Q 160 MET cc_start: 0.8498 (ttp) cc_final: 0.7913 (ttp) REVERT: R 144 CYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6388 (p) REVERT: S 33 MET cc_start: 0.8369 (mpp) cc_final: 0.7962 (mpp) REVERT: S 45 LYS cc_start: 0.7731 (tptp) cc_final: 0.7437 (mtpm) REVERT: T 3 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.3787 (ptm-80) REVERT: T 47 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7955 (mt) REVERT: T 74 ASN cc_start: 0.8449 (p0) cc_final: 0.8204 (p0) REVERT: U 13 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6972 (tm) REVERT: U 15 ASP cc_start: 0.7803 (t0) cc_final: 0.7482 (t70) REVERT: U 23 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8460 (tp-100) REVERT: U 34 ARG cc_start: 0.8414 (tpp80) cc_final: 0.8211 (tpt-90) REVERT: U 53 ASP cc_start: 0.8832 (p0) cc_final: 0.8368 (p0) REVERT: W 11 TYR cc_start: 0.8448 (t80) cc_final: 0.8175 (t80) REVERT: W 18 THR cc_start: 0.8411 (t) cc_final: 0.7940 (m) REVERT: W 30 LEU cc_start: 0.8613 (mt) cc_final: 0.8399 (mt) REVERT: X 32 LEU cc_start: 0.8635 (tp) cc_final: 0.8420 (tt) REVERT: X 39 ARG cc_start: 0.5409 (pmt170) cc_final: 0.4236 (mpp-170) outliers start: 198 outliers final: 71 residues processed: 534 average time/residue: 0.4885 time to fit residues: 326.4256 Evaluate side-chains 418 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 325 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 TRP Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 446 PHE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 345 HIS Chi-restraints excluded: chain Q residue 212 MET Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 68 CYS Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 274 optimal weight: 4.9990 chunk 73 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 chunk 345 optimal weight: 2.9990 chunk 158 optimal weight: 0.0870 chunk 380 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 246 optimal weight: 2.9990 chunk 384 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 295 optimal weight: 0.0970 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 GLN A 430 GLN B 170 ASN B 240 HIS B 247 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN E 121 GLN E 149 ASN G 80 ASN N 240 GLN N 430 GLN O 31 ASN O 170 ASN O 247 GLN O 284 HIS Q 71 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.125866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.099451 restraints weight = 61768.324| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.42 r_work: 0.3346 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.327 34693 Z= 0.122 Angle : 0.622 23.687 47173 Z= 0.298 Chirality : 0.041 0.208 5168 Planarity : 0.004 0.102 6040 Dihedral : 6.802 88.661 4759 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.49 % Favored : 95.23 % Rotamer: Outliers : 5.15 % Allowed : 27.63 % Favored : 67.21 % 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: 0.31 (0.13), residues: 4234 helix: 1.27 (0.11), residues: 2044 sheet: -0.16 (0.27), residues: 391 loop : -0.94 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 36 TYR 0.020 0.001 TYR A 434 PHE 0.018 0.001 PHE A 324 TRP 0.022 0.001 TRP P 163 HIS 0.005 0.001 HIS O 240 Details of bonding type rmsd covalent geometry : bond 0.00280 (34674) covalent geometry : angle 0.60517 (47156) SS BOND : bond 0.00516 ( 5) SS BOND : angle 2.57371 ( 10) hydrogen bonds : bond 0.03889 ( 1722) hydrogen bonds : angle 4.62678 ( 4935) metal coordination : bond 0.00813 ( 8) metal coordination : angle 11.57543 ( 7) Misc. bond : bond 0.17115 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 357 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7289 (t80) REVERT: A 77 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7638 (mttm) REVERT: A 136 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7778 (tp-100) REVERT: A 320 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7899 (tp) REVERT: A 342 TRP cc_start: 0.8087 (m-10) cc_final: 0.7449 (m-10) REVERT: B 110 GLU cc_start: 0.8110 (tt0) cc_final: 0.7786 (tt0) REVERT: B 156 GLN cc_start: 0.8275 (pt0) cc_final: 0.7933 (pp30) REVERT: B 354 ASN cc_start: 0.8552 (t0) cc_final: 0.8275 (t0) REVERT: B 407 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6964 (t0) REVERT: B 424 MET cc_start: 0.7943 (tpp) cc_final: 0.7670 (ttt) REVERT: C 8 HIS cc_start: 0.0791 (OUTLIER) cc_final: 0.0331 (t70) REVERT: C 155 TYR cc_start: 0.7456 (t80) cc_final: 0.6713 (t80) REVERT: C 211 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7823 (mm) REVERT: C 316 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6958 (mtm) REVERT: D 17 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8612 (tp) REVERT: D 41 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7206 (t-90) REVERT: D 82 MET cc_start: 0.8427 (mmm) cc_final: 0.7573 (mmt) REVERT: E 118 ARG cc_start: 0.1052 (OUTLIER) cc_final: -0.3564 (ttt180) REVERT: E 192 MET cc_start: 0.5775 (tpp) cc_final: 0.5419 (mmt) REVERT: F 100 ARG cc_start: 0.7670 (ttp80) cc_final: 0.7203 (ttp-110) REVERT: H 53 ASP cc_start: 0.8552 (p0) cc_final: 0.8059 (p0) REVERT: H 69 VAL cc_start: 0.8343 (t) cc_final: 0.8092 (t) REVERT: I 2 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7937 (mt) REVERT: I 16 SER cc_start: 0.6401 (OUTLIER) cc_final: 0.6154 (p) REVERT: I 20 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.5350 (ptp90) REVERT: J 1 MET cc_start: 0.1617 (mtt) cc_final: 0.0998 (mtm) REVERT: J 45 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7661 (mm-30) REVERT: K 47 TYR cc_start: 0.4748 (OUTLIER) cc_final: 0.4533 (t80) REVERT: O 200 THR cc_start: 0.8564 (p) cc_final: 0.8362 (p) REVERT: O 430 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7691 (mt) REVERT: P 75 TYR cc_start: 0.7840 (m-80) cc_final: 0.7555 (m-80) REVERT: P 164 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7816 (mp) REVERT: P 216 ASP cc_start: 0.7090 (t70) cc_final: 0.6838 (t70) REVERT: P 268 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7622 (pp) REVERT: P 345 HIS cc_start: 0.6359 (OUTLIER) cc_final: 0.4747 (p-80) REVERT: Q 31 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7613 (mm-40) REVERT: Q 160 MET cc_start: 0.8508 (ttp) cc_final: 0.7914 (ttp) REVERT: R 53 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6942 (m110) REVERT: R 96 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7296 (pp) REVERT: S 12 ARG cc_start: -0.0381 (OUTLIER) cc_final: -0.2009 (pmt-80) REVERT: S 33 MET cc_start: 0.8377 (mpp) cc_final: 0.7991 (mpp) REVERT: S 45 LYS cc_start: 0.7782 (tptp) cc_final: 0.7471 (mtpm) REVERT: T 1 MET cc_start: -0.0166 (mpt) cc_final: -0.0371 (mpt) REVERT: T 3 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.3661 (ptm-80) REVERT: T 47 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8037 (mt) REVERT: T 74 ASN cc_start: 0.8464 (p0) cc_final: 0.8232 (p0) REVERT: U 13 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6886 (tm) REVERT: U 15 ASP cc_start: 0.7618 (t0) cc_final: 0.7242 (t70) REVERT: U 23 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8634 (tp-100) REVERT: U 34 ARG cc_start: 0.8531 (tpp80) cc_final: 0.8309 (tpp80) REVERT: U 53 ASP cc_start: 0.8837 (p0) cc_final: 0.8381 (p0) REVERT: W 11 TYR cc_start: 0.8464 (t80) cc_final: 0.8192 (t80) REVERT: W 18 THR cc_start: 0.8496 (t) cc_final: 0.8032 (m) REVERT: W 30 LEU cc_start: 0.8612 (mt) cc_final: 0.8402 (mt) REVERT: X 39 ARG cc_start: 0.5689 (pmt170) cc_final: 0.4338 (mpp-170) REVERT: X 48 ILE cc_start: 0.4947 (OUTLIER) cc_final: 0.4450 (mt) outliers start: 185 outliers final: 72 residues processed: 501 average time/residue: 0.5209 time to fit residues: 323.9631 Evaluate side-chains 422 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 324 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 165 TYR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 20 ARG Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 38 TRP Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain O residue 430 LEU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 328 LEU Chi-restraints excluded: chain P residue 345 HIS Chi-restraints excluded: chain Q residue 212 MET Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 68 CYS Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 240 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 260 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 265 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 391 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 323 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN B 197 ASN B 240 HIS C 3 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN H 67 HIS N 240 GLN N 328 HIS ** N 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 GLN O 284 HIS P 8 HIS T 24 GLN U 67 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.092190 restraints weight = 62036.840| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.59 r_work: 0.3196 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.439 34693 Z= 0.178 Angle : 0.678 19.314 47173 Z= 0.330 Chirality : 0.045 0.270 5168 Planarity : 0.005 0.100 6040 Dihedral : 6.962 89.199 4756 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.27 % Favored : 94.45 % Rotamer: Outliers : 5.63 % Allowed : 26.85 % Favored : 67.52 % 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: 0.15 (0.13), residues: 4234 helix: 1.14 (0.11), residues: 2049 sheet: -0.28 (0.27), residues: 393 loop : -1.02 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 206 TYR 0.018 0.002 TYR A 434 PHE 0.024 0.002 PHE A 336 TRP 0.029 0.002 TRP P 163 HIS 0.006 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00417 (34674) covalent geometry : angle 0.66366 (47156) SS BOND : bond 0.00592 ( 5) SS BOND : angle 2.02936 ( 10) hydrogen bonds : bond 0.04301 ( 1722) hydrogen bonds : angle 4.68408 ( 4935) metal coordination : bond 0.03283 ( 8) metal coordination : angle 10.99499 ( 7) Misc. bond : bond 0.22162 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 349 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.7797 (m) REVERT: B 120 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8138 (mtm) REVERT: B 140 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8267 (tp) REVERT: B 354 ASN cc_start: 0.8603 (t0) cc_final: 0.8274 (t0) REVERT: B 407 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.6826 (t0) REVERT: C 57 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8512 (m) REVERT: C 155 TYR cc_start: 0.7425 (t80) cc_final: 0.6625 (t80) REVERT: C 175 LEU cc_start: 0.7840 (tp) cc_final: 0.7636 (tp) REVERT: C 211 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7388 (mm) REVERT: C 214 ASP cc_start: 0.7722 (m-30) cc_final: 0.7518 (m-30) REVERT: C 255 ASN cc_start: 0.8279 (t0) cc_final: 0.8070 (t0) REVERT: C 357 LEU cc_start: 0.7979 (tp) cc_final: 0.7704 (tt) REVERT: C 366 MET cc_start: 0.6502 (mtt) cc_final: 0.6189 (mmt) REVERT: D 15 ARG cc_start: 0.7698 (ttp80) cc_final: 0.6976 (ptm160) REVERT: D 17 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8601 (tp) REVERT: D 75 ASN cc_start: 0.8055 (t0) cc_final: 0.7173 (p0) REVERT: D 82 MET cc_start: 0.8365 (mmm) cc_final: 0.7352 (mmt) REVERT: D 160 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7397 (ttt) REVERT: D 211 MET cc_start: 0.8443 (tpt) cc_final: 0.8190 (tpt) REVERT: E 37 TYR cc_start: 0.8073 (m-10) cc_final: 0.7763 (m-10) REVERT: E 118 ARG cc_start: 0.1794 (OUTLIER) cc_final: -0.3342 (ttt180) REVERT: F 40 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: F 100 ARG cc_start: 0.7377 (ttp80) cc_final: 0.7003 (ttp-110) REVERT: H 53 ASP cc_start: 0.8600 (p0) cc_final: 0.7763 (p0) REVERT: I 2 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7866 (mt) REVERT: I 16 SER cc_start: 0.6638 (OUTLIER) cc_final: 0.6303 (p) REVERT: I 20 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.5409 (ptp90) REVERT: J 45 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: K 17 TRP cc_start: 0.7424 (m100) cc_final: 0.7202 (m100) REVERT: K 47 TYR cc_start: 0.4767 (OUTLIER) cc_final: 0.4445 (t80) REVERT: N 307 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7142 (t80) REVERT: N 345 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8351 (mm) REVERT: O 424 MET cc_start: 0.8413 (ttt) cc_final: 0.8160 (ttt) REVERT: O 438 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: P 102 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8686 (mm) REVERT: P 162 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: P 216 ASP cc_start: 0.7700 (t70) cc_final: 0.7447 (t70) REVERT: P 282 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8130 (mtp85) REVERT: P 345 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.4676 (p-80) REVERT: Q 71 GLN cc_start: 0.8151 (tt0) cc_final: 0.7874 (pt0) REVERT: Q 75 ASN cc_start: 0.7659 (t0) cc_final: 0.7443 (t0) REVERT: Q 204 MET cc_start: 0.8783 (mtm) cc_final: 0.8575 (mtm) REVERT: R 37 TYR cc_start: 0.7547 (m-80) cc_final: 0.7128 (m-80) REVERT: R 53 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6946 (m110) REVERT: R 78 LEU cc_start: 0.7042 (pt) cc_final: 0.6440 (mp) REVERT: R 89 PHE cc_start: 0.6851 (p90) cc_final: 0.6435 (p90) REVERT: R 96 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6892 (pp) REVERT: S 12 ARG cc_start: -0.0693 (OUTLIER) cc_final: -0.2304 (pmt-80) REVERT: S 22 TYR cc_start: 0.8671 (t80) cc_final: 0.8215 (t80) REVERT: S 33 MET cc_start: 0.8425 (mpp) cc_final: 0.7871 (mpp) REVERT: S 99 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7353 (mp) REVERT: T 3 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.3941 (ptm-80) REVERT: U 13 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6968 (tm) REVERT: U 15 ASP cc_start: 0.7540 (t0) cc_final: 0.7139 (t70) REVERT: U 23 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8419 (tp-100) REVERT: U 53 ASP cc_start: 0.8882 (p0) cc_final: 0.8321 (p0) REVERT: W 30 LEU cc_start: 0.8216 (mt) cc_final: 0.7985 (mt) outliers start: 202 outliers final: 96 residues processed: 505 average time/residue: 0.5081 time to fit residues: 317.9601 Evaluate side-chains 419 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 295 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 20 ARG Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 33 GLU Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 TRP Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 446 PHE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain O residue 430 LEU Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 172 LYS Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 331 ASP Chi-restraints excluded: chain P residue 345 HIS Chi-restraints excluded: chain Q residue 212 MET Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 99 ILE Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 17 TYR Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 347 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 378 optimal weight: 0.8980 chunk 360 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 195 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 182 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 118 GLN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN E 121 GLN G 74 ASN G 80 ASN N 430 GLN O 284 HIS P 16 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 HIS T 24 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.120970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.092752 restraints weight = 61765.450| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.60 r_work: 0.3209 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.479 34693 Z= 0.148 Angle : 0.635 17.632 47173 Z= 0.307 Chirality : 0.043 0.225 5168 Planarity : 0.004 0.100 6040 Dihedral : 6.723 89.480 4751 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.56 % Favored : 95.18 % Rotamer: Outliers : 5.40 % Allowed : 27.55 % Favored : 67.05 % 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: 0.27 (0.13), residues: 4234 helix: 1.26 (0.11), residues: 2053 sheet: -0.16 (0.27), residues: 375 loop : -0.99 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 36 TYR 0.018 0.001 TYR A 4 PHE 0.020 0.001 PHE B 324 TRP 0.023 0.001 TRP P 163 HIS 0.005 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00352 (34674) covalent geometry : angle 0.62166 (47156) SS BOND : bond 0.00279 ( 5) SS BOND : angle 1.72895 ( 10) hydrogen bonds : bond 0.03888 ( 1722) hydrogen bonds : angle 4.58287 ( 4935) metal coordination : bond 0.01485 ( 8) metal coordination : angle 10.49555 ( 7) Misc. bond : bond 0.22419 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 308 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7939 (tp) REVERT: C 129 MET cc_start: 0.7875 (mtm) cc_final: 0.7436 (mtm) REVERT: C 155 TYR cc_start: 0.7528 (t80) cc_final: 0.6740 (t80) REVERT: C 175 LEU cc_start: 0.8018 (tp) cc_final: 0.7807 (tp) REVERT: C 211 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7256 (mm) REVERT: C 345 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.6039 (p-80) REVERT: C 357 LEU cc_start: 0.7903 (tp) cc_final: 0.7646 (tt) REVERT: C 366 MET cc_start: 0.6559 (mtt) cc_final: 0.6274 (mmt) REVERT: D 15 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7052 (ptm160) REVERT: D 17 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8652 (tp) REVERT: D 40 CYS cc_start: 0.7637 (m) cc_final: 0.7278 (m) REVERT: D 82 MET cc_start: 0.8480 (mmm) cc_final: 0.7408 (mmt) REVERT: D 211 MET cc_start: 0.8579 (tpt) cc_final: 0.8369 (tpt) REVERT: E 37 TYR cc_start: 0.8077 (m-10) cc_final: 0.7809 (m-10) REVERT: E 140 THR cc_start: 0.6195 (OUTLIER) cc_final: 0.5994 (p) REVERT: F 15 GLU cc_start: 0.8435 (tp30) cc_final: 0.7942 (tp30) REVERT: F 45 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7084 (mtpm) REVERT: G 48 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7693 (mpp80) REVERT: H 32 LYS cc_start: 0.8746 (tppp) cc_final: 0.8456 (tppp) REVERT: H 53 ASP cc_start: 0.8695 (p0) cc_final: 0.7818 (p0) REVERT: I 1 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.4464 (mmm) REVERT: I 2 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7870 (mt) REVERT: I 16 SER cc_start: 0.6443 (OUTLIER) cc_final: 0.6092 (p) REVERT: J 33 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8500 (pt0) REVERT: J 41 ASP cc_start: 0.8173 (m-30) cc_final: 0.7969 (m-30) REVERT: J 45 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: K 47 TYR cc_start: 0.4803 (OUTLIER) cc_final: 0.4493 (t80) REVERT: N 244 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7533 (ttt-90) REVERT: N 307 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7116 (t80) REVERT: N 345 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8187 (mm) REVERT: O 120 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.6946 (mpp) REVERT: O 424 MET cc_start: 0.8555 (ttt) cc_final: 0.8347 (ttt) REVERT: P 282 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8215 (mtp85) REVERT: P 345 HIS cc_start: 0.6649 (OUTLIER) cc_final: 0.4627 (p-80) REVERT: Q 4 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6707 (tp30) REVERT: R 37 TYR cc_start: 0.7540 (m-80) cc_final: 0.7107 (m-80) REVERT: R 78 LEU cc_start: 0.7273 (pt) cc_final: 0.6461 (mp) REVERT: R 96 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7053 (pp) REVERT: S 12 ARG cc_start: -0.1142 (OUTLIER) cc_final: -0.2644 (pmt-80) REVERT: S 22 TYR cc_start: 0.8519 (t80) cc_final: 0.8249 (t80) REVERT: S 33 MET cc_start: 0.8396 (mpp) cc_final: 0.7952 (mpp) REVERT: S 45 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7351 (mtpm) REVERT: T 3 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.4030 (ptm-80) REVERT: U 15 ASP cc_start: 0.7512 (t0) cc_final: 0.7226 (t70) REVERT: U 23 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8495 (tp-100) REVERT: U 53 ASP cc_start: 0.8886 (p0) cc_final: 0.8420 (p0) REVERT: W 30 LEU cc_start: 0.8223 (mt) cc_final: 0.8008 (mt) outliers start: 194 outliers final: 88 residues processed: 460 average time/residue: 0.5175 time to fit residues: 293.6419 Evaluate side-chains 406 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 294 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 165 TYR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 48 ARG Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 33 GLU Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 38 TRP Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 240 GLN Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 244 ARG Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 446 PHE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 172 LYS Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 341 GLN Chi-restraints excluded: chain P residue 345 HIS Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 212 MET Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 17 TYR Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 194 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 222 GLN B 240 HIS ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN G 13 HIS G 74 ASN G 80 ASN ** N 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 GLN Q 71 GLN T 24 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.115834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.087588 restraints weight = 62707.988| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.56 r_work: 0.3116 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.7217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.608 34693 Z= 0.306 Angle : 0.790 20.882 47173 Z= 0.387 Chirality : 0.049 0.286 5168 Planarity : 0.006 0.099 6040 Dihedral : 7.162 88.695 4747 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.07 % Favored : 93.65 % Rotamer: Outliers : 5.54 % Allowed : 27.66 % Favored : 66.80 % 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: -0.28 (0.13), residues: 4234 helix: 0.74 (0.11), residues: 2044 sheet: -0.51 (0.26), residues: 408 loop : -1.15 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 206 TYR 0.027 0.002 TYR P 81 PHE 0.023 0.003 PHE A 336 TRP 0.033 0.002 TRP C 31 HIS 0.010 0.002 HIS O 277 Details of bonding type rmsd covalent geometry : bond 0.00730 (34674) covalent geometry : angle 0.77393 (47156) SS BOND : bond 0.00901 ( 5) SS BOND : angle 2.21535 ( 10) hydrogen bonds : bond 0.04995 ( 1722) hydrogen bonds : angle 4.98711 ( 4935) metal coordination : bond 0.01422 ( 8) metal coordination : angle 12.72819 ( 7) Misc. bond : bond 0.30002 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 289 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8418 (tp) REVERT: A 291 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8071 (t) REVERT: B 120 MET cc_start: 0.8157 (mtm) cc_final: 0.7797 (mtp) REVERT: B 246 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: C 155 TYR cc_start: 0.7554 (t80) cc_final: 0.6805 (t80) REVERT: C 209 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8528 (p) REVERT: C 345 HIS cc_start: 0.7586 (OUTLIER) cc_final: 0.5697 (p-80) REVERT: C 366 MET cc_start: 0.7249 (mtt) cc_final: 0.6984 (mmt) REVERT: C 375 LYS cc_start: 0.8743 (mttp) cc_final: 0.8033 (ttpt) REVERT: D 17 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8406 (tp) REVERT: D 40 CYS cc_start: 0.7707 (m) cc_final: 0.7388 (m) REVERT: D 82 MET cc_start: 0.8480 (mmm) cc_final: 0.7467 (mmt) REVERT: D 160 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7462 (ttt) REVERT: D 211 MET cc_start: 0.8797 (tpt) cc_final: 0.8549 (tpt) REVERT: E 37 TYR cc_start: 0.8061 (m-10) cc_final: 0.7750 (m-10) REVERT: H 32 LYS cc_start: 0.8769 (tppp) cc_final: 0.8455 (tppp) REVERT: H 53 ASP cc_start: 0.8792 (p0) cc_final: 0.7968 (p0) REVERT: I 16 SER cc_start: 0.6762 (OUTLIER) cc_final: 0.6408 (p) REVERT: J 45 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7617 (mm-30) REVERT: N 197 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7961 (tt) REVERT: N 307 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7495 (t80) REVERT: O 102 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7783 (mpt180) REVERT: O 120 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7223 (mpp) REVERT: O 424 MET cc_start: 0.8385 (ttt) cc_final: 0.8148 (ttt) REVERT: P 102 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8517 (mm) REVERT: P 282 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8182 (mtp85) REVERT: P 345 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.5206 (p-80) REVERT: Q 75 ASN cc_start: 0.7830 (t0) cc_final: 0.7568 (t0) REVERT: Q 142 SER cc_start: 0.8447 (m) cc_final: 0.8025 (p) REVERT: R 37 TYR cc_start: 0.7488 (m-80) cc_final: 0.7084 (m-80) REVERT: R 78 LEU cc_start: 0.7384 (pt) cc_final: 0.6646 (mp) REVERT: R 96 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7106 (pp) REVERT: S 12 ARG cc_start: -0.0851 (OUTLIER) cc_final: -0.2239 (pmt-80) REVERT: S 33 MET cc_start: 0.8497 (mpp) cc_final: 0.7880 (mpp) REVERT: S 86 GLU cc_start: 0.7986 (mp0) cc_final: 0.7670 (pt0) REVERT: S 103 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7375 (tppp) REVERT: S 108 TRP cc_start: 0.7536 (t-100) cc_final: 0.7285 (t-100) REVERT: T 3 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.4087 (ptm-80) REVERT: U 15 ASP cc_start: 0.7608 (t0) cc_final: 0.7240 (t70) REVERT: U 23 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8622 (tp-100) REVERT: U 53 ASP cc_start: 0.8887 (p0) cc_final: 0.8421 (p0) REVERT: V 47 ARG cc_start: 0.6100 (ppt170) cc_final: 0.5652 (ppt170) REVERT: W 45 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: X 1 MET cc_start: 0.3360 (OUTLIER) cc_final: 0.2788 (ptt) outliers start: 199 outliers final: 94 residues processed: 443 average time/residue: 0.5401 time to fit residues: 293.1770 Evaluate side-chains 382 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 266 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 TRP Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 446 PHE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 102 ARG Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 172 LYS Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 284 ILE Chi-restraints excluded: chain P residue 287 LYS Chi-restraints excluded: chain P residue 345 HIS Chi-restraints excluded: chain Q residue 212 MET Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 17 TYR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 18 optimal weight: 0.8980 chunk 262 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 229 optimal weight: 0.7980 chunk 385 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 GLN Q 71 GLN T 7 HIS T 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.090532 restraints weight = 61749.149| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.56 r_work: 0.3167 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.512 34693 Z= 0.158 Angle : 0.674 19.371 47173 Z= 0.326 Chirality : 0.044 0.215 5168 Planarity : 0.005 0.099 6040 Dihedral : 6.893 89.780 4743 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.72 % Favored : 94.97 % Rotamer: Outliers : 3.79 % Allowed : 29.81 % Favored : 66.41 % 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: 0.02 (0.13), residues: 4234 helix: 1.07 (0.11), residues: 2044 sheet: -0.46 (0.26), residues: 417 loop : -1.10 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 206 TYR 0.022 0.001 TYR A 4 PHE 0.019 0.002 PHE B 324 TRP 0.025 0.002 TRP P 163 HIS 0.007 0.001 HIS G 13 Details of bonding type rmsd covalent geometry : bond 0.00378 (34674) covalent geometry : angle 0.65770 (47156) SS BOND : bond 0.00517 ( 5) SS BOND : angle 1.67491 ( 10) hydrogen bonds : bond 0.04104 ( 1722) hydrogen bonds : angle 4.72657 ( 4935) metal coordination : bond 0.01041 ( 8) metal coordination : angle 11.95138 ( 7) Misc. bond : bond 0.25256 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 290 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.8279 (mtm) cc_final: 0.8007 (mtm) REVERT: C 82 MET cc_start: 0.8192 (mtp) cc_final: 0.7608 (mtt) REVERT: C 155 TYR cc_start: 0.7564 (t80) cc_final: 0.6832 (t80) REVERT: C 209 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8546 (p) REVERT: C 240 MET cc_start: 0.9002 (mmt) cc_final: 0.8677 (mmm) REVERT: C 345 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.5558 (p-80) REVERT: C 366 MET cc_start: 0.7061 (mtt) cc_final: 0.6784 (mmt) REVERT: C 375 LYS cc_start: 0.8626 (mttp) cc_final: 0.8001 (tttt) REVERT: D 17 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8422 (tp) REVERT: D 40 CYS cc_start: 0.7422 (m) cc_final: 0.7126 (m) REVERT: D 82 MET cc_start: 0.8452 (mmm) cc_final: 0.7465 (mmt) REVERT: D 160 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7502 (ttt) REVERT: D 211 MET cc_start: 0.8712 (tpt) cc_final: 0.8395 (tpt) REVERT: F 15 GLU cc_start: 0.8292 (tp30) cc_final: 0.7923 (tp30) REVERT: H 53 ASP cc_start: 0.8839 (p0) cc_final: 0.7972 (p0) REVERT: I 1 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.4611 (mmm) REVERT: I 16 SER cc_start: 0.6741 (OUTLIER) cc_final: 0.6397 (p) REVERT: J 45 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: N 176 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8527 (mmtt) REVERT: N 307 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7277 (t80) REVERT: O 102 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7833 (mpt180) REVERT: O 120 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7645 (mtt) REVERT: P 49 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8952 (tp) REVERT: P 216 ASP cc_start: 0.8110 (t70) cc_final: 0.7892 (t70) REVERT: P 331 ASP cc_start: 0.8119 (t0) cc_final: 0.7787 (t0) REVERT: P 345 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.5036 (p-80) REVERT: Q 75 ASN cc_start: 0.7608 (t0) cc_final: 0.7355 (t0) REVERT: Q 142 SER cc_start: 0.8396 (m) cc_final: 0.7974 (p) REVERT: R 37 TYR cc_start: 0.7529 (m-80) cc_final: 0.7133 (m-80) REVERT: R 78 LEU cc_start: 0.7344 (pt) cc_final: 0.6636 (mp) REVERT: R 96 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7285 (pp) REVERT: S 12 ARG cc_start: -0.0704 (OUTLIER) cc_final: -0.2273 (pmt-80) REVERT: S 33 MET cc_start: 0.8407 (mpp) cc_final: 0.7981 (mpp) REVERT: S 86 GLU cc_start: 0.7974 (mp0) cc_final: 0.7768 (pt0) REVERT: T 3 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.4135 (ptm-80) REVERT: U 15 ASP cc_start: 0.7449 (t0) cc_final: 0.7200 (t70) REVERT: U 23 GLN cc_start: 0.9034 (tp-100) cc_final: 0.8617 (tp-100) REVERT: U 53 ASP cc_start: 0.8908 (p0) cc_final: 0.8464 (p0) REVERT: V 47 ARG cc_start: 0.6002 (ppt170) cc_final: 0.5767 (ppt170) REVERT: W 1 MET cc_start: 0.3319 (mmm) cc_final: 0.2951 (mpp) REVERT: W 45 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7481 (mp0) outliers start: 136 outliers final: 73 residues processed: 404 average time/residue: 0.5309 time to fit residues: 264.6140 Evaluate side-chains 360 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 271 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 TRP Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 446 PHE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 102 ARG Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 345 HIS Chi-restraints excluded: chain Q residue 212 MET Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain X residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 293 optimal weight: 0.9990 chunk 288 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 339 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 181 optimal weight: 0.0970 chunk 236 optimal weight: 0.8980 chunk 258 optimal weight: 0.8980 chunk 310 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN G 80 ASN N 430 GLN Q 71 GLN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.119366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.091661 restraints weight = 61439.545| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.48 r_work: 0.3190 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.7410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.516 34693 Z= 0.138 Angle : 0.657 18.031 47173 Z= 0.316 Chirality : 0.043 0.247 5168 Planarity : 0.004 0.099 6040 Dihedral : 6.720 89.232 4742 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.24 % Favored : 94.45 % Rotamer: Outliers : 3.26 % Allowed : 30.45 % Favored : 66.30 % 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: 0.17 (0.13), residues: 4234 helix: 1.21 (0.11), residues: 2046 sheet: -0.39 (0.26), residues: 417 loop : -1.04 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 206 TYR 0.021 0.001 TYR A 4 PHE 0.024 0.001 PHE A 336 TRP 0.030 0.001 TRP C 163 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00327 (34674) covalent geometry : angle 0.64246 (47156) SS BOND : bond 0.00280 ( 5) SS BOND : angle 1.72901 ( 10) hydrogen bonds : bond 0.03894 ( 1722) hydrogen bonds : angle 4.61928 ( 4935) metal coordination : bond 0.00923 ( 8) metal coordination : angle 11.07525 ( 7) Misc. bond : bond 0.24843 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 290 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8161 (tpp) cc_final: 0.7210 (mpp) REVERT: A 206 ARG cc_start: 0.8607 (ttm110) cc_final: 0.8289 (ttp-110) REVERT: A 291 SER cc_start: 0.8399 (OUTLIER) cc_final: 0.7992 (t) REVERT: A 297 ILE cc_start: 0.7794 (mp) cc_final: 0.7576 (mt) REVERT: B 120 MET cc_start: 0.8257 (mtm) cc_final: 0.7712 (mtm) REVERT: B 238 LYS cc_start: 0.7686 (ptpp) cc_final: 0.7303 (mppt) REVERT: C 82 MET cc_start: 0.8183 (mtp) cc_final: 0.7795 (mtp) REVERT: C 155 TYR cc_start: 0.7505 (t80) cc_final: 0.6752 (t80) REVERT: C 209 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8453 (p) REVERT: C 240 MET cc_start: 0.9021 (mmt) cc_final: 0.8740 (mmm) REVERT: C 345 HIS cc_start: 0.7524 (OUTLIER) cc_final: 0.5501 (p-80) REVERT: C 366 MET cc_start: 0.7021 (mtt) cc_final: 0.6779 (mmt) REVERT: C 375 LYS cc_start: 0.8592 (mttp) cc_final: 0.7974 (tttt) REVERT: D 17 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8399 (tp) REVERT: D 40 CYS cc_start: 0.7389 (m) cc_final: 0.7113 (m) REVERT: D 82 MET cc_start: 0.8416 (mmm) cc_final: 0.7450 (mmt) REVERT: D 160 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7764 (ttt) REVERT: D 211 MET cc_start: 0.8698 (tpt) cc_final: 0.8270 (tpt) REVERT: E 81 ILE cc_start: 0.5349 (OUTLIER) cc_final: 0.4659 (tp) REVERT: E 87 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6456 (tpp) REVERT: F 15 GLU cc_start: 0.8306 (tp30) cc_final: 0.7932 (tp30) REVERT: H 53 ASP cc_start: 0.8840 (p0) cc_final: 0.7969 (p0) REVERT: I 16 SER cc_start: 0.6412 (OUTLIER) cc_final: 0.6037 (p) REVERT: J 45 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7603 (mm-30) REVERT: K 16 ASN cc_start: 0.5212 (m-40) cc_final: 0.4915 (m-40) REVERT: N 176 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8559 (mmtt) REVERT: N 307 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7272 (t80) REVERT: O 120 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7624 (mtt) REVERT: O 238 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7393 (pttm) REVERT: P 49 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8925 (tp) REVERT: P 331 ASP cc_start: 0.8069 (t0) cc_final: 0.7753 (t0) REVERT: P 345 HIS cc_start: 0.7059 (OUTLIER) cc_final: 0.4954 (p-80) REVERT: Q 75 ASN cc_start: 0.7643 (t0) cc_final: 0.7365 (t0) REVERT: R 37 TYR cc_start: 0.7554 (m-80) cc_final: 0.7191 (m-80) REVERT: R 78 LEU cc_start: 0.7250 (pt) cc_final: 0.6517 (mp) REVERT: R 96 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7259 (pp) REVERT: S 12 ARG cc_start: -0.0728 (OUTLIER) cc_final: -0.2466 (pmt-80) REVERT: S 33 MET cc_start: 0.8480 (mpp) cc_final: 0.7889 (mpp) REVERT: T 3 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.4197 (ptm-80) REVERT: T 66 GLU cc_start: 0.8807 (tp30) cc_final: 0.8536 (tp30) REVERT: U 15 ASP cc_start: 0.7438 (t0) cc_final: 0.7152 (t70) REVERT: U 23 GLN cc_start: 0.9022 (tp-100) cc_final: 0.8614 (tp-100) REVERT: U 53 ASP cc_start: 0.8911 (p0) cc_final: 0.8474 (p0) REVERT: V 47 ARG cc_start: 0.6008 (ppt170) cc_final: 0.5783 (ppt170) REVERT: W 1 MET cc_start: 0.3507 (mmm) cc_final: 0.3260 (mpp) REVERT: W 45 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7320 (mp0) outliers start: 117 outliers final: 73 residues processed: 385 average time/residue: 0.5499 time to fit residues: 259.2203 Evaluate side-chains 357 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 267 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 48 ARG Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 TRP Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 446 PHE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 345 HIS Chi-restraints excluded: chain Q residue 212 MET Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 17 TYR Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 83 optimal weight: 0.9980 chunk 167 optimal weight: 0.0970 chunk 221 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 347 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 GLN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.119399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.091635 restraints weight = 62103.504| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.55 r_work: 0.3186 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.7544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.516 34693 Z= 0.145 Angle : 0.660 17.580 47173 Z= 0.318 Chirality : 0.043 0.243 5168 Planarity : 0.004 0.099 6040 Dihedral : 6.638 87.176 4742 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.05 % Favored : 94.64 % Rotamer: Outliers : 3.20 % Allowed : 30.61 % Favored : 66.18 % 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: 0.18 (0.13), residues: 4234 helix: 1.21 (0.11), residues: 2061 sheet: -0.30 (0.26), residues: 411 loop : -1.07 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 39 TYR 0.020 0.001 TYR A 4 PHE 0.018 0.001 PHE B 324 TRP 0.034 0.001 TRP C 163 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00346 (34674) covalent geometry : angle 0.64711 (47156) SS BOND : bond 0.00445 ( 5) SS BOND : angle 1.68024 ( 10) hydrogen bonds : bond 0.03857 ( 1722) hydrogen bonds : angle 4.57575 ( 4935) metal coordination : bond 0.00905 ( 8) metal coordination : angle 10.60615 ( 7) Misc. bond : bond 0.24560 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 280 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8611 (ttm110) cc_final: 0.8302 (ttp-110) REVERT: A 291 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.7993 (t) REVERT: B 120 MET cc_start: 0.8223 (mtm) cc_final: 0.7807 (mtm) REVERT: C 82 MET cc_start: 0.8187 (mtp) cc_final: 0.7815 (mtp) REVERT: C 148 ASN cc_start: 0.8060 (m-40) cc_final: 0.7312 (t0) REVERT: C 155 TYR cc_start: 0.7445 (t80) cc_final: 0.6651 (t80) REVERT: C 209 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8502 (p) REVERT: C 240 MET cc_start: 0.9009 (mmt) cc_final: 0.8766 (mmm) REVERT: C 345 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.5645 (p-80) REVERT: C 366 MET cc_start: 0.7031 (mtt) cc_final: 0.6798 (mmt) REVERT: C 375 LYS cc_start: 0.8559 (mttp) cc_final: 0.7949 (tttt) REVERT: D 17 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8479 (tp) REVERT: D 31 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7596 (mt0) REVERT: D 40 CYS cc_start: 0.7431 (m) cc_final: 0.7165 (m) REVERT: D 82 MET cc_start: 0.8396 (mmm) cc_final: 0.7408 (mmt) REVERT: D 160 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7698 (ttt) REVERT: D 211 MET cc_start: 0.8707 (tpt) cc_final: 0.8260 (tpt) REVERT: E 81 ILE cc_start: 0.5371 (OUTLIER) cc_final: 0.4643 (tp) REVERT: H 53 ASP cc_start: 0.8853 (p0) cc_final: 0.7985 (p0) REVERT: I 16 SER cc_start: 0.6391 (OUTLIER) cc_final: 0.6029 (p) REVERT: I 20 ARG cc_start: 0.7321 (pmm-80) cc_final: 0.5949 (pmm150) REVERT: J 41 ASP cc_start: 0.8110 (m-30) cc_final: 0.7892 (m-30) REVERT: J 45 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7616 (mm-30) REVERT: K 16 ASN cc_start: 0.5329 (m-40) cc_final: 0.5075 (m-40) REVERT: N 220 SER cc_start: 0.8871 (t) cc_final: 0.8485 (p) REVERT: N 307 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7351 (t80) REVERT: O 120 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7825 (mtt) REVERT: P 46 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8885 (mm) REVERT: P 49 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8920 (tp) REVERT: P 331 ASP cc_start: 0.8091 (t0) cc_final: 0.7774 (t0) REVERT: P 345 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.5024 (p-80) REVERT: Q 75 ASN cc_start: 0.7656 (t0) cc_final: 0.7362 (t0) REVERT: R 37 TYR cc_start: 0.7556 (m-80) cc_final: 0.7203 (m-80) REVERT: R 78 LEU cc_start: 0.7252 (pt) cc_final: 0.6540 (mp) REVERT: R 96 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7242 (pp) REVERT: S 12 ARG cc_start: -0.0707 (OUTLIER) cc_final: -0.2228 (pmt-80) REVERT: S 33 MET cc_start: 0.8505 (mpp) cc_final: 0.7887 (mpp) REVERT: T 3 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.4991 (ptm-80) REVERT: T 66 GLU cc_start: 0.8803 (tp30) cc_final: 0.8486 (tp30) REVERT: U 15 ASP cc_start: 0.7368 (t0) cc_final: 0.7064 (t70) REVERT: U 23 GLN cc_start: 0.9041 (tp-100) cc_final: 0.8616 (tp-100) REVERT: U 53 ASP cc_start: 0.8909 (p0) cc_final: 0.8478 (p0) REVERT: W 45 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: X 39 ARG cc_start: 0.5759 (pmt170) cc_final: 0.4303 (mpp-170) outliers start: 115 outliers final: 79 residues processed: 380 average time/residue: 0.5506 time to fit residues: 255.4076 Evaluate side-chains 366 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 270 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 48 ARG Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 TRP Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 446 PHE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 343 VAL Chi-restraints excluded: chain P residue 345 HIS Chi-restraints excluded: chain Q residue 212 MET Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 17 TYR Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 0.4980 chunk 108 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 339 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 368 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 GLN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.091659 restraints weight = 61220.169| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.53 r_work: 0.3186 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.7602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.512 34693 Z= 0.147 Angle : 0.660 17.488 47173 Z= 0.318 Chirality : 0.043 0.249 5168 Planarity : 0.004 0.098 6040 Dihedral : 6.618 86.485 4742 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.13 % Favored : 94.57 % Rotamer: Outliers : 3.29 % Allowed : 30.47 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.13), residues: 4234 helix: 1.24 (0.11), residues: 2057 sheet: -0.29 (0.26), residues: 411 loop : -1.07 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 39 TYR 0.020 0.001 TYR A 4 PHE 0.019 0.001 PHE A 336 TRP 0.038 0.002 TRP C 163 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00351 (34674) covalent geometry : angle 0.64592 (47156) SS BOND : bond 0.00446 ( 5) SS BOND : angle 1.59734 ( 10) hydrogen bonds : bond 0.03844 ( 1722) hydrogen bonds : angle 4.55388 ( 4935) metal coordination : bond 0.00898 ( 8) metal coordination : angle 10.85995 ( 7) Misc. bond : bond 0.25039 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8783.74 seconds wall clock time: 151 minutes 5.15 seconds (9065.15 seconds total)