Starting phenix.real_space_refine on Sat Jun 28 19:02:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p65_17461/06_2025/8p65_17461.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p65_17461/06_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_17461/06_2025/8p65_17461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p65_17461/06_2025/8p65_17461.map" model { file = "/net/cci-nas-00/data/ceres_data/8p65_17461/06_2025/8p65_17461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p65_17461/06_2025/8p65_17461.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.65, per 1000 atoms: 0.61 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: 9.11 Conformation dependent library (CDL) restraints added in 4.7 seconds 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: 3.92 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: 12.49 Time building geometry restraints manager: 10.81 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: 0.04 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: 1.910 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: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 86.150 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.270 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:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.260 ------------------------------------------------------------------------------- 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 : 10.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), 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 TRP 0.029 0.001 TRP A 443 HIS 0.006 0.001 HIS A 328 PHE 0.023 0.001 PHE A 336 TYR 0.018 0.001 TYR P 224 ARG 0.007 0.000 ARG I 20 Details of bonding type rmsd hydrogen bonds : bond 0.25685 ( 1722) hydrogen bonds : angle 7.98134 ( 4935) metal coordination : bond 0.00623 ( 8) metal coordination : angle 11.33553 ( 7) SS BOND : bond 0.02169 ( 5) SS BOND : angle 2.77360 ( 10) covalent geometry : bond 0.00360 (34674) covalent geometry : angle 0.61864 (47156) 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 : 4.084 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 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: 0.5999 (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: 0.6464 (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: 0.7269 (tp30) REVERT: B 392 TYR cc_start: 0.4853 (t80) cc_final: 0.4166 (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: 0.6847 (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: 0.7252 (m-10) REVERT: E 62 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6920 (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: 0.3446 (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: 0.7749 (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: 0.7410 (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: 0.6329 (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: 0.7576 (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: 0.7327 (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: 0.6996 (m-80) REVERT: R 181 GLU cc_start: 0.4347 (tm-30) cc_final: 0.4125 (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: 0.6378 (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: 0.6797 (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: 57 residues processed: 896 average time/residue: 1.1207 time to fit residues: 1256.3351 Evaluate side-chains 516 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 448 time to evaluate : 3.562 ------------------------------------------------------------------------------- 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 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 351 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 242 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 143 GLN B 174 ASN B 240 HIS B 247 GLN B 297 GLN D 31 GLN D 166 ASN E 149 ASN G 7 HIS G 24 GLN G 80 ASN H 67 HIS J 48 ASN K 16 ASN N 240 GLN N 430 GLN O 20 HIS O 174 ASN O 247 GLN O 284 HIS P 74 ASN P 207 ASN Q 31 GLN Q 71 GLN ** Q 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 GLN W 48 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.124386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096432 restraints weight = 62538.506| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.54 r_work: 0.3298 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.469 34693 Z= 0.281 Angle : 0.867 32.869 47173 Z= 0.430 Chirality : 0.050 0.228 5168 Planarity : 0.006 0.104 6040 Dihedral : 8.061 88.802 4826 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.36 % Favored : 94.33 % Rotamer: Outliers : 7.74 % Allowed : 25.96 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4234 helix: 0.35 (0.11), residues: 2063 sheet: -0.28 (0.26), residues: 391 loop : -1.19 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 342 HIS 0.015 0.002 HIS A 85 PHE 0.027 0.003 PHE B 378 TYR 0.041 0.002 TYR A 434 ARG 0.011 0.001 ARG V 20 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 1722) hydrogen bonds : angle 5.33055 ( 4935) metal coordination : bond 0.02087 ( 8) metal coordination : angle 16.10508 ( 7) SS BOND : bond 0.00256 ( 5) SS BOND : angle 1.36074 ( 10) covalent geometry : bond 0.00644 (34674) covalent geometry : angle 0.84492 (47156) Misc. bond : bond 0.29782 ( 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 675 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 397 time to evaluate : 3.884 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 343 MET cc_start: 0.4963 (OUTLIER) cc_final: 0.3930 (ptt) REVERT: A 351 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6945 (mm-30) REVERT: A 443 TRP cc_start: 0.3631 (t-100) cc_final: 0.3298 (t-100) REVERT: B 110 GLU cc_start: 0.8065 (tt0) cc_final: 0.7817 (tt0) REVERT: B 136 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8599 (mt-10) REVERT: B 223 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.5511 (p90) REVERT: B 376 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7397 (tm-30) REVERT: B 385 GLN cc_start: 0.7166 (mt0) cc_final: 0.6707 (mt0) REVERT: B 424 MET cc_start: 0.8047 (tpp) cc_final: 0.7752 (ttt) REVERT: C 57 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8511 (m) REVERT: C 75 TYR cc_start: 0.8530 (m-80) cc_final: 0.8307 (m-80) REVERT: C 110 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8504 (mm) REVERT: C 155 TYR cc_start: 0.7406 (t80) cc_final: 0.6709 (t80) REVERT: C 234 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7577 (mt) REVERT: C 373 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: D 82 MET cc_start: 0.8349 (mmm) cc_final: 0.8003 (mmp) REVERT: D 212 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7707 (mtt) REVERT: E 37 TYR cc_start: 0.7771 (m-10) cc_final: 0.7443 (m-10) REVERT: E 118 ARG cc_start: 0.1408 (OUTLIER) cc_final: -0.3492 (ttt180) REVERT: E 192 MET cc_start: 0.5520 (tpp) cc_final: 0.5304 (mmt) REVERT: F 97 GLU cc_start: 0.7443 (tp30) cc_final: 0.6953 (tp30) REVERT: F 100 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7281 (ttp80) REVERT: G 4 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: G 12 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7964 (mtp85) REVERT: H 32 LYS cc_start: 0.8869 (tppp) cc_final: 0.8484 (tppp) REVERT: H 53 ASP cc_start: 0.8530 (p0) cc_final: 0.8256 (p0) REVERT: I 2 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8285 (mp) REVERT: J 1 MET cc_start: 0.1494 (OUTLIER) cc_final: 0.0938 (mtt) REVERT: J 16 ARG cc_start: 0.7777 (tpp80) cc_final: 0.7531 (tpt170) REVERT: J 45 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7807 (mm-30) REVERT: K 22 SER cc_start: 0.4202 (OUTLIER) cc_final: 0.3730 (p) REVERT: N 19 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8718 (tt) REVERT: N 99 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8238 (mp) REVERT: N 307 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.6886 (t80) REVERT: N 415 PHE cc_start: 0.8218 (m-10) cc_final: 0.7968 (m-10) REVERT: O 96 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8117 (tt) REVERT: O 105 MET cc_start: 0.8315 (ttt) cc_final: 0.7974 (ttm) REVERT: O 146 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8146 (tt) REVERT: O 200 THR cc_start: 0.8749 (p) cc_final: 0.8508 (p) REVERT: O 278 VAL cc_start: 0.8643 (t) cc_final: 0.8284 (t) REVERT: O 326 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8602 (t) REVERT: O 438 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: P 46 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9030 (mm) REVERT: P 75 TYR cc_start: 0.8351 (m-80) cc_final: 0.8042 (m-80) REVERT: P 138 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8479 (mmp) REVERT: P 216 ASP cc_start: 0.7556 (t70) cc_final: 0.7333 (t70) REVERT: P 345 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.4966 (p-80) REVERT: Q 160 MET cc_start: 0.8335 (ttp) cc_final: 0.7714 (ttp) REVERT: R 60 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8314 (t) REVERT: R 136 ILE cc_start: 0.8484 (pp) cc_final: 0.8250 (mm) REVERT: R 144 CYS cc_start: 0.6440 (OUTLIER) cc_final: 0.6006 (p) REVERT: S 33 MET cc_start: 0.8624 (mpp) cc_final: 0.8149 (mpp) REVERT: S 45 LYS cc_start: 0.8014 (tptp) cc_final: 0.7757 (mtpm) REVERT: S 99 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7444 (mp) REVERT: T 3 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.4153 (ptm-80) REVERT: T 68 GLU cc_start: 0.7761 (tp30) cc_final: 0.7554 (mm-30) REVERT: T 74 ASN cc_start: 0.8524 (p0) cc_final: 0.8257 (p0) REVERT: U 13 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6927 (tm) REVERT: U 23 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8440 (mt0) REVERT: U 53 ASP cc_start: 0.8965 (p0) cc_final: 0.8626 (p0) REVERT: W 7 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7241 (m) REVERT: W 18 THR cc_start: 0.8536 (t) cc_final: 0.8007 (m) REVERT: X 39 ARG cc_start: 0.5949 (pmt170) cc_final: 0.4826 (mpp-170) outliers start: 278 outliers final: 93 residues processed: 621 average time/residue: 1.1914 time to fit residues: 926.3465 Evaluate side-chains 445 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 322 time to evaluate : 4.426 ------------------------------------------------------------------------------- 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 127 ILE 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 343 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 261 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 B residue 418 VAL Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 273 TYR Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 356 VAL 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 212 MET 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 40 GLU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain G residue 4 GLN 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 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 1 MET Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 38 TRP Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 313 CYS Chi-restraints excluded: chain N residue 376 CYS 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 76 THR 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 438 GLU Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 138 MET 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 284 ILE Chi-restraints excluded: chain P residue 345 HIS Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain R residue 60 SER 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 99 ILE Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 70 SER 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 4 VAL 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 139 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 277 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 352 optimal weight: 1.9990 chunk 297 optimal weight: 0.4980 chunk 305 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 379 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 368 HIS A 430 GLN B 170 ASN B 240 HIS B 343 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS E 121 GLN G 24 GLN G 80 ASN I 31 GLN N 328 HIS N 430 GLN P 8 HIS P 207 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.124870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096769 restraints weight = 62325.530| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.56 r_work: 0.3303 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.398 34693 Z= 0.143 Angle : 0.661 30.747 47173 Z= 0.317 Chirality : 0.043 0.343 5168 Planarity : 0.005 0.105 6040 Dihedral : 7.321 89.597 4774 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.61 % Favored : 95.11 % Rotamer: Outliers : 5.96 % Allowed : 26.99 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4234 helix: 0.94 (0.11), residues: 2050 sheet: -0.15 (0.27), residues: 379 loop : -1.11 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 163 HIS 0.005 0.001 HIS T 7 PHE 0.022 0.001 PHE N 336 TYR 0.022 0.001 TYR A 434 ARG 0.007 0.000 ARG H 36 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 1722) hydrogen bonds : angle 4.89155 ( 4935) metal coordination : bond 0.00882 ( 8) metal coordination : angle 14.42634 ( 7) SS BOND : bond 0.00522 ( 5) SS BOND : angle 1.72315 ( 10) covalent geometry : bond 0.00331 (34674) covalent geometry : angle 0.63719 (47156) Misc. bond : bond 0.20232 ( 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 566 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 352 time to evaluate : 3.639 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 58 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: A 77 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7940 (mttm) REVERT: A 291 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8154 (t) REVERT: A 351 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 120 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.6766 (mpp) REVERT: B 376 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7511 (tm-30) REVERT: B 407 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.6988 (t0) REVERT: C 57 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8500 (m) REVERT: C 75 TYR cc_start: 0.8535 (m-80) cc_final: 0.8261 (m-80) REVERT: C 155 TYR cc_start: 0.7455 (t80) cc_final: 0.6879 (t80) REVERT: C 248 ASP cc_start: 0.8059 (t0) cc_final: 0.7808 (m-30) REVERT: C 278 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7891 (t80) REVERT: C 316 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7491 (ttt) REVERT: C 373 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: D 17 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8576 (tp) REVERT: D 82 MET cc_start: 0.8447 (mmm) cc_final: 0.7938 (mmp) REVERT: D 160 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.6984 (ttt) REVERT: D 211 MET cc_start: 0.8504 (tpt) cc_final: 0.8229 (tpt) REVERT: E 37 TYR cc_start: 0.8008 (m-10) cc_final: 0.7649 (m-10) REVERT: E 118 ARG cc_start: 0.1569 (OUTLIER) cc_final: -0.3136 (ttt180) REVERT: E 192 MET cc_start: 0.5607 (tpp) cc_final: 0.5286 (mmt) REVERT: F 40 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: F 100 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7603 (ttp80) REVERT: G 4 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: H 53 ASP cc_start: 0.8560 (p0) cc_final: 0.8113 (p0) REVERT: I 2 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8148 (mp) REVERT: I 16 SER cc_start: 0.6732 (OUTLIER) cc_final: 0.6501 (p) REVERT: I 20 ARG cc_start: 0.6132 (OUTLIER) cc_final: 0.5335 (ptp90) REVERT: J 1 MET cc_start: 0.1856 (OUTLIER) cc_final: 0.1292 (ptp) REVERT: J 23 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7560 (mm) REVERT: J 33 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8317 (pt0) REVERT: J 45 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7858 (mm-30) REVERT: N 307 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.6977 (t80) REVERT: O 105 MET cc_start: 0.8465 (ttt) cc_final: 0.8182 (ttm) REVERT: O 326 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8683 (t) REVERT: O 424 MET cc_start: 0.8635 (ttt) cc_final: 0.8341 (ttt) REVERT: O 438 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: P 46 LEU cc_start: 0.9262 (tp) cc_final: 0.9052 (mm) REVERT: P 75 TYR cc_start: 0.8197 (m-80) cc_final: 0.7891 (m-80) REVERT: P 164 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7854 (mp) REVERT: P 216 ASP cc_start: 0.7508 (t70) cc_final: 0.7262 (t70) REVERT: P 345 HIS cc_start: 0.6851 (OUTLIER) cc_final: 0.4795 (p-80) REVERT: Q 160 MET cc_start: 0.8576 (ttp) cc_final: 0.8152 (ttp) REVERT: R 12 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8146 (t70) REVERT: R 53 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.6597 (m110) REVERT: R 78 LEU cc_start: 0.7010 (pt) cc_final: 0.6391 (mp) REVERT: R 89 PHE cc_start: 0.7056 (p90) cc_final: 0.6848 (p90) REVERT: R 96 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7130 (pp) REVERT: R 136 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8299 (mm) REVERT: R 144 CYS cc_start: 0.5880 (OUTLIER) cc_final: 0.5452 (p) REVERT: S 12 ARG cc_start: -0.0295 (OUTLIER) cc_final: -0.1912 (pmt-80) REVERT: S 33 MET cc_start: 0.8459 (mpp) cc_final: 0.7950 (mpp) REVERT: S 65 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7821 (ptt-90) REVERT: T 74 ASN cc_start: 0.8422 (p0) cc_final: 0.8199 (p0) REVERT: U 13 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7074 (tm) REVERT: U 15 ASP cc_start: 0.7683 (t0) cc_final: 0.7290 (t70) REVERT: U 23 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8674 (tp-100) REVERT: U 34 ARG cc_start: 0.8453 (tpp80) cc_final: 0.8130 (tpp80) REVERT: U 53 ASP cc_start: 0.8847 (p0) cc_final: 0.8379 (p0) REVERT: V 42 VAL cc_start: 0.5269 (OUTLIER) cc_final: 0.5001 (m) REVERT: W 7 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7283 (m) REVERT: X 39 ARG cc_start: 0.5659 (pmt170) cc_final: 0.4352 (mpp-170) outliers start: 214 outliers final: 69 residues processed: 514 average time/residue: 1.2021 time to fit residues: 765.3646 Evaluate side-chains 411 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 306 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 58 PHE 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 149 VAL Chi-restraints excluded: chain A residue 186 LEU 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 B residue 89 ILE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 261 SER 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 203 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 273 TYR Chi-restraints excluded: chain C residue 278 TYR 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 D residue 160 MET 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 F residue 40 GLU Chi-restraints excluded: chain G residue 4 GLN Chi-restraints excluded: chain G residue 8 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 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 1 MET Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 23 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 N residue 17 SER Chi-restraints excluded: chain N residue 127 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 8 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 326 THR Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain P residue 110 LEU 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 239 LEU Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 284 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 Q residue 214 LEU Chi-restraints excluded: chain R residue 12 ASP 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 136 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 65 ARG Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 87 ASP 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 13 LEU Chi-restraints excluded: chain U residue 68 CYS 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 V residue 30 VAL Chi-restraints excluded: chain V residue 42 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 344 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 303 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 362 optimal weight: 5.9990 chunk 365 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN G 80 ASN H 23 GLN H 26 GLN N 240 GLN N 328 HIS N 430 GLN O 170 ASN O 240 HIS O 284 HIS Q 71 GLN T 24 GLN U 67 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.123845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.095591 restraints weight = 62185.007| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.54 r_work: 0.3283 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.442 34693 Z= 0.165 Angle : 0.666 27.303 47173 Z= 0.320 Chirality : 0.044 0.321 5168 Planarity : 0.005 0.103 6040 Dihedral : 7.110 87.581 4761 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.98 % Favored : 94.73 % Rotamer: Outliers : 5.93 % Allowed : 26.94 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 4234 helix: 1.07 (0.11), residues: 2037 sheet: -0.14 (0.27), residues: 379 loop : -1.10 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP P 163 HIS 0.006 0.001 HIS N 61 PHE 0.019 0.002 PHE A 324 TYR 0.021 0.001 TYR A 434 ARG 0.007 0.001 ARG U 36 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 1722) hydrogen bonds : angle 4.73852 ( 4935) metal coordination : bond 0.00887 ( 8) metal coordination : angle 13.13890 ( 7) SS BOND : bond 0.00988 ( 5) SS BOND : angle 1.41718 ( 10) covalent geometry : bond 0.00393 (34674) covalent geometry : angle 0.64614 (47156) Misc. bond : bond 0.21766 ( 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 539 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 326 time to evaluate : 3.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: A 75 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.7993 (tp) REVERT: A 291 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8048 (m) REVERT: A 351 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7392 (mm-30) REVERT: A 355 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7345 (mt) REVERT: B 120 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7678 (mtt) REVERT: B 376 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7570 (tp30) REVERT: B 407 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7649 (m-30) REVERT: C 57 SER cc_start: 0.8888 (OUTLIER) cc_final: 0.8563 (m) REVERT: C 75 TYR cc_start: 0.8464 (m-80) cc_final: 0.8038 (m-80) REVERT: C 155 TYR cc_start: 0.7581 (t80) cc_final: 0.6928 (t80) REVERT: C 209 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8519 (p) REVERT: C 248 ASP cc_start: 0.8270 (t0) cc_final: 0.8034 (m-30) REVERT: C 273 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8737 (p90) REVERT: C 345 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.6282 (p-80) REVERT: C 366 MET cc_start: 0.7140 (mtt) cc_final: 0.6900 (mmt) REVERT: C 373 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: D 17 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8664 (tp) REVERT: D 40 CYS cc_start: 0.7636 (m) cc_final: 0.7300 (m) REVERT: D 82 MET cc_start: 0.8508 (mmm) cc_final: 0.7909 (mmp) REVERT: D 160 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.6916 (ttt) REVERT: D 211 MET cc_start: 0.8762 (tpt) cc_final: 0.8298 (tpt) REVERT: E 37 TYR cc_start: 0.8165 (m-10) cc_final: 0.7858 (m-10) REVERT: E 118 ARG cc_start: 0.1690 (OUTLIER) cc_final: -0.3121 (ttt180) REVERT: F 100 ARG cc_start: 0.7786 (ttp80) cc_final: 0.7456 (ttp80) REVERT: G 4 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: H 23 GLN cc_start: 0.6541 (mm-40) cc_final: 0.5858 (pp30) REVERT: H 32 LYS cc_start: 0.9092 (tppp) cc_final: 0.8729 (tppp) REVERT: H 53 ASP cc_start: 0.8676 (p0) cc_final: 0.7853 (p0) REVERT: I 2 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8154 (mp) REVERT: I 16 SER cc_start: 0.6564 (OUTLIER) cc_final: 0.6330 (p) REVERT: J 1 MET cc_start: 0.1514 (OUTLIER) cc_final: 0.1013 (ptp) REVERT: J 23 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7224 (mm) REVERT: J 33 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8493 (pt0) REVERT: J 45 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: N 244 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7531 (ttt-90) REVERT: N 307 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7164 (t80) REVERT: O 120 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7063 (mpp) REVERT: O 326 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8765 (t) REVERT: O 438 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: P 46 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9119 (mm) REVERT: P 162 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: P 216 ASP cc_start: 0.7968 (t70) cc_final: 0.7736 (t70) REVERT: P 331 ASP cc_start: 0.8062 (t0) cc_final: 0.7712 (t0) REVERT: P 345 HIS cc_start: 0.6877 (OUTLIER) cc_final: 0.4928 (p-80) REVERT: R 12 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8138 (t70) REVERT: R 37 TYR cc_start: 0.7668 (m-80) cc_final: 0.7319 (m-80) REVERT: R 78 LEU cc_start: 0.7170 (pt) cc_final: 0.6431 (mp) REVERT: R 89 PHE cc_start: 0.7026 (p90) cc_final: 0.6758 (p90) REVERT: R 96 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7120 (pp) REVERT: R 136 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8466 (mm) REVERT: S 12 ARG cc_start: -0.0408 (OUTLIER) cc_final: -0.2171 (pmt-80) REVERT: S 22 TYR cc_start: 0.8704 (t80) cc_final: 0.8406 (t80) REVERT: S 33 MET cc_start: 0.8535 (mpp) cc_final: 0.8093 (mpp) REVERT: S 99 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7689 (mp) REVERT: U 13 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7021 (tm) REVERT: U 15 ASP cc_start: 0.7395 (t0) cc_final: 0.7001 (t70) REVERT: U 23 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8323 (tp-100) REVERT: U 29 LYS cc_start: 0.8307 (ttmm) cc_final: 0.7924 (mtmm) REVERT: U 34 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8114 (tpp80) REVERT: U 53 ASP cc_start: 0.8919 (p0) cc_final: 0.8409 (p0) REVERT: V 47 ARG cc_start: 0.5693 (ppt170) cc_final: 0.5360 (ppt170) outliers start: 213 outliers final: 92 residues processed: 497 average time/residue: 1.2155 time to fit residues: 749.4791 Evaluate side-chains 418 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 291 time to evaluate : 3.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 277 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 355 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 372 VAL 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 57 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 200 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 233 LEU Chi-restraints excluded: chain C residue 273 TYR Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain D residue 17 LEU 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 E residue 45 VAL Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain G residue 4 GLN 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 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 1 MET 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 23 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 N residue 17 SER Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 240 GLN 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 309 THR 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 76 THR 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 305 GLU Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 326 THR Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 46 LEU 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 211 ILE Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 284 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 Q residue 214 LEU Chi-restraints excluded: chain R residue 12 ASP Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 136 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 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 19 LEU Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 13 LEU 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 V residue 30 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain W residue 7 THR 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 338 optimal weight: 1.9990 chunk 352 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 405 optimal weight: 0.0370 chunk 218 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 316 optimal weight: 0.0030 chunk 410 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 366 optimal weight: 9.9990 overall best weight: 0.7672 ------------------------------------------------------------------------------- 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 B 174 ASN B 197 ASN B 240 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN G 80 ASN N 328 HIS N 430 GLN P 8 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.123908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095722 restraints weight = 61962.535| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.53 r_work: 0.3286 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.539 34693 Z= 0.144 Angle : 0.638 25.399 47173 Z= 0.307 Chirality : 0.043 0.331 5168 Planarity : 0.004 0.103 6040 Dihedral : 6.855 87.950 4755 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.96 % Favored : 94.76 % Rotamer: Outliers : 5.93 % Allowed : 27.16 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 4234 helix: 1.21 (0.11), residues: 2038 sheet: -0.12 (0.27), residues: 379 loop : -1.04 (0.15), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 132 HIS 0.006 0.001 HIS N 328 PHE 0.022 0.001 PHE A 336 TYR 0.022 0.001 TYR A 4 ARG 0.015 0.000 ARG I 20 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 1722) hydrogen bonds : angle 4.66053 ( 4935) metal coordination : bond 0.00890 ( 8) metal coordination : angle 12.47193 ( 7) SS BOND : bond 0.00603 ( 5) SS BOND : angle 1.56057 ( 10) covalent geometry : bond 0.00344 (34674) covalent geometry : angle 0.61909 (47156) Misc. bond : bond 0.24604 ( 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 518 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 305 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9116 (tp) REVERT: A 58 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: A 75 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8069 (tp) REVERT: A 291 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8078 (m) REVERT: A 351 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7440 (mm-30) REVERT: B 120 MET cc_start: 0.8273 (tpp) cc_final: 0.7963 (mtt) REVERT: B 376 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7548 (tp30) REVERT: B 407 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7699 (m-30) REVERT: C 57 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8593 (m) REVERT: C 75 TYR cc_start: 0.8459 (m-80) cc_final: 0.8047 (m-80) REVERT: C 129 MET cc_start: 0.7988 (mtm) cc_final: 0.7532 (mtm) REVERT: C 155 TYR cc_start: 0.7515 (t80) cc_final: 0.6816 (t80) REVERT: C 248 ASP cc_start: 0.8310 (t0) cc_final: 0.8052 (m-30) REVERT: C 273 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.8733 (p90) REVERT: C 345 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.6315 (p-80) REVERT: C 366 MET cc_start: 0.7307 (mtt) cc_final: 0.7087 (mmt) REVERT: C 373 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: D 17 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8666 (tp) REVERT: D 40 CYS cc_start: 0.7505 (m) cc_final: 0.7226 (m) REVERT: D 82 MET cc_start: 0.8552 (mmm) cc_final: 0.7896 (mmp) REVERT: D 160 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.6972 (ttt) REVERT: D 211 MET cc_start: 0.8823 (tpt) cc_final: 0.8512 (tpt) REVERT: E 37 TYR cc_start: 0.8151 (m-10) cc_final: 0.7836 (m-10) REVERT: E 75 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: E 118 ARG cc_start: 0.1614 (OUTLIER) cc_final: -0.3175 (ttt180) REVERT: F 100 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7306 (ttp80) REVERT: G 4 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: H 53 ASP cc_start: 0.8721 (p0) cc_final: 0.7884 (p0) REVERT: I 2 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8138 (mp) REVERT: I 16 SER cc_start: 0.6431 (OUTLIER) cc_final: 0.6126 (p) REVERT: J 1 MET cc_start: 0.0988 (OUTLIER) cc_final: 0.0504 (ptp) REVERT: J 33 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: J 45 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: N 240 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8850 (tt0) REVERT: N 307 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7174 (t80) REVERT: O 120 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7017 (mpp) REVERT: O 326 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8788 (t) REVERT: O 424 MET cc_start: 0.8459 (ttt) cc_final: 0.8250 (ttt) REVERT: P 162 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6393 (mp0) REVERT: P 164 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8272 (mm) REVERT: P 331 ASP cc_start: 0.8053 (t0) cc_final: 0.7717 (t0) REVERT: P 345 HIS cc_start: 0.6963 (OUTLIER) cc_final: 0.5001 (p-80) REVERT: Q 4 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6747 (tp30) REVERT: Q 71 GLN cc_start: 0.8369 (tt0) cc_final: 0.7798 (tm-30) REVERT: R 37 TYR cc_start: 0.7622 (m-80) cc_final: 0.7224 (m-80) REVERT: R 78 LEU cc_start: 0.7125 (pt) cc_final: 0.6419 (mp) REVERT: R 89 PHE cc_start: 0.7146 (p90) cc_final: 0.6656 (p90) REVERT: R 96 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7132 (pp) REVERT: R 136 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8492 (mm) REVERT: R 194 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7163 (mm) REVERT: S 12 ARG cc_start: -0.0622 (OUTLIER) cc_final: -0.2337 (pmt-80) REVERT: S 22 TYR cc_start: 0.8698 (t80) cc_final: 0.8415 (t80) REVERT: S 33 MET cc_start: 0.8521 (mpp) cc_final: 0.8124 (mpp) REVERT: S 65 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7814 (ptt-90) REVERT: S 108 TRP cc_start: 0.7461 (t-100) cc_final: 0.7163 (t-100) REVERT: T 1 MET cc_start: 0.1271 (OUTLIER) cc_final: 0.0939 (mpt) REVERT: T 3 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5345 (ptm160) REVERT: T 71 LYS cc_start: 0.8786 (mtpt) cc_final: 0.8510 (mtmt) REVERT: U 13 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7065 (tm) REVERT: U 15 ASP cc_start: 0.7347 (t0) cc_final: 0.7099 (t70) REVERT: U 23 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8365 (tp-100) REVERT: U 29 LYS cc_start: 0.8257 (ttmm) cc_final: 0.7919 (mtmm) REVERT: U 34 ARG cc_start: 0.8357 (tpp80) cc_final: 0.8114 (tpp80) REVERT: U 53 ASP cc_start: 0.8915 (p0) cc_final: 0.8504 (p0) REVERT: V 47 ARG cc_start: 0.5766 (ppt170) cc_final: 0.5457 (ppt170) outliers start: 213 outliers final: 94 residues processed: 471 average time/residue: 1.1179 time to fit residues: 659.5722 Evaluate side-chains 412 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 282 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 VAL 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 351 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 261 SER 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 407 ASP Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 13 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 273 TYR Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 17 LEU 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 75 GLU 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 F residue 14 LEU Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain G residue 4 GLN 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 H residue 14 VAL 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 1 MET 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 N residue 17 SER Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 240 GLN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 309 THR 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 76 THR Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 326 THR Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 39 ILE 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 164 ILE 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 284 ILE Chi-restraints excluded: chain P residue 310 SER Chi-restraints excluded: chain P residue 316 MET 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 R residue 96 LEU Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 65 ARG Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 13 LEU 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 V residue 30 VAL Chi-restraints excluded: chain W residue 6 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 134 optimal weight: 0.0970 chunk 213 optimal weight: 0.0050 chunk 314 optimal weight: 0.0980 chunk 167 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 243 optimal weight: 0.8980 chunk 316 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 129 optimal weight: 0.2980 overall best weight: 0.2592 ------------------------------------------------------------------------------- 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN B 240 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN E 121 GLN G 74 ASN G 80 ASN N 240 GLN N 328 HIS N 430 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.123043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094880 restraints weight = 61585.932| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.61 r_work: 0.3242 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.455 34693 Z= 0.116 Angle : 0.624 20.107 47173 Z= 0.300 Chirality : 0.042 0.316 5168 Planarity : 0.004 0.103 6040 Dihedral : 6.645 88.434 4753 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.77 % Favored : 94.95 % Rotamer: Outliers : 4.65 % Allowed : 28.36 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.13), residues: 4234 helix: 1.40 (0.11), residues: 2045 sheet: -0.05 (0.28), residues: 375 loop : -1.03 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP P 163 HIS 0.004 0.001 HIS A 252 PHE 0.019 0.001 PHE A 336 TYR 0.021 0.001 TYR A 4 ARG 0.009 0.000 ARG H 36 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 1722) hydrogen bonds : angle 4.49408 ( 4935) metal coordination : bond 0.00886 ( 8) metal coordination : angle 10.49509 ( 7) SS BOND : bond 0.00417 ( 5) SS BOND : angle 3.58357 ( 10) covalent geometry : bond 0.00264 (34674) covalent geometry : angle 0.60840 (47156) Misc. bond : bond 0.20843 ( 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 490 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 323 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7235 (mm-30) REVERT: B 120 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7598 (mtm) REVERT: B 238 LYS cc_start: 0.7462 (ptpp) cc_final: 0.6928 (mtmt) REVERT: B 376 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7457 (tp30) REVERT: B 407 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: C 75 TYR cc_start: 0.8423 (m-80) cc_final: 0.7975 (m-80) REVERT: C 129 MET cc_start: 0.7820 (mtm) cc_final: 0.7256 (mtp) REVERT: C 155 TYR cc_start: 0.7547 (t80) cc_final: 0.6783 (t80) REVERT: C 248 ASP cc_start: 0.8323 (t0) cc_final: 0.7992 (m-30) REVERT: C 273 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8589 (p90) REVERT: C 345 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.6476 (p-80) REVERT: C 366 MET cc_start: 0.6698 (mtt) cc_final: 0.6454 (mmt) REVERT: D 40 CYS cc_start: 0.7419 (m) cc_final: 0.7120 (m) REVERT: D 82 MET cc_start: 0.8501 (mmm) cc_final: 0.7709 (mmp) REVERT: D 160 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6787 (ttt) REVERT: D 211 MET cc_start: 0.8597 (tpt) cc_final: 0.8303 (tpt) REVERT: F 100 ARG cc_start: 0.7544 (ttp80) cc_final: 0.7078 (ttp80) REVERT: G 48 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7852 (mpp80) REVERT: H 31 VAL cc_start: 0.8370 (p) cc_final: 0.8080 (m) REVERT: H 53 ASP cc_start: 0.8706 (p0) cc_final: 0.7777 (p0) REVERT: I 2 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7862 (mp) REVERT: I 16 SER cc_start: 0.6329 (OUTLIER) cc_final: 0.5999 (p) REVERT: J 33 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: J 41 ASP cc_start: 0.8165 (m-30) cc_final: 0.7951 (m-30) REVERT: J 45 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7672 (mm-30) REVERT: N 307 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7144 (t80) REVERT: O 95 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7844 (ttmm) REVERT: O 120 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.6935 (mpp) REVERT: O 326 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8650 (t) REVERT: O 438 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: P 162 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: P 216 ASP cc_start: 0.7795 (t70) cc_final: 0.7480 (t70) REVERT: P 331 ASP cc_start: 0.7863 (t0) cc_final: 0.7613 (t0) REVERT: P 345 HIS cc_start: 0.6719 (OUTLIER) cc_final: 0.5120 (p-80) REVERT: Q 71 GLN cc_start: 0.8448 (tt0) cc_final: 0.7867 (tm-30) REVERT: R 37 TYR cc_start: 0.7494 (m-80) cc_final: 0.7022 (m-80) REVERT: R 78 LEU cc_start: 0.7184 (pt) cc_final: 0.6458 (mp) REVERT: R 96 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6707 (pp) REVERT: R 136 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8397 (mm) REVERT: S 12 ARG cc_start: -0.0877 (OUTLIER) cc_final: -0.2468 (pmt-80) REVERT: S 33 MET cc_start: 0.8432 (mpp) cc_final: 0.7839 (mpp) REVERT: S 108 TRP cc_start: 0.7230 (t-100) cc_final: 0.6944 (t-100) REVERT: T 1 MET cc_start: 0.1217 (OUTLIER) cc_final: 0.0767 (mpt) REVERT: T 3 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.5278 (ptm160) REVERT: U 15 ASP cc_start: 0.7522 (t0) cc_final: 0.7215 (t70) REVERT: U 23 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8512 (tp-100) REVERT: U 29 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7880 (mtmm) REVERT: U 34 ARG cc_start: 0.8346 (tpp80) cc_final: 0.8132 (tpp80) REVERT: U 53 ASP cc_start: 0.8904 (p0) cc_final: 0.8437 (p0) REVERT: X 39 ARG cc_start: 0.5484 (pmt170) cc_final: 0.4196 (mpp-170) outliers start: 167 outliers final: 64 residues processed: 450 average time/residue: 1.2834 time to fit residues: 715.8208 Evaluate side-chains 369 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 284 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 VAL 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 120 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 261 SER 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 407 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 273 TYR Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 377 LEU 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 133 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 9 THR 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 2 LEU 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 38 TRP Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 127 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 O residue 4 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 310 SER Chi-restraints excluded: chain O residue 326 THR Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 171 ASP 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 98 VAL Chi-restraints excluded: chain R residue 136 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 S residue 95 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 17 TYR Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain W residue 7 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 132 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 365 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 369 optimal weight: 7.9990 chunk 364 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B 240 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** N 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 GLN W 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.120943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.092440 restraints weight = 62250.744| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.60 r_work: 0.3202 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.548 34693 Z= 0.148 Angle : 0.642 18.424 47173 Z= 0.309 Chirality : 0.043 0.350 5168 Planarity : 0.004 0.101 6040 Dihedral : 6.554 87.523 4743 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.96 % Favored : 94.73 % Rotamer: Outliers : 4.54 % Allowed : 28.75 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.13), residues: 4234 helix: 1.43 (0.11), residues: 2039 sheet: -0.06 (0.28), residues: 370 loop : -1.01 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP P 163 HIS 0.007 0.001 HIS N 328 PHE 0.016 0.001 PHE C 91 TYR 0.018 0.001 TYR A 434 ARG 0.007 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 1722) hydrogen bonds : angle 4.53546 ( 4935) metal coordination : bond 0.00931 ( 8) metal coordination : angle 10.29716 ( 7) SS BOND : bond 0.00526 ( 5) SS BOND : angle 1.73533 ( 10) covalent geometry : bond 0.00356 (34674) covalent geometry : angle 0.62926 (47156) Misc. bond : bond 0.24769 ( 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 456 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 293 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7297 (mm-30) REVERT: B 120 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7917 (mtt) REVERT: B 238 LYS cc_start: 0.7479 (ptpp) cc_final: 0.6946 (mtmt) REVERT: B 376 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7479 (tp30) REVERT: B 407 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: C 75 TYR cc_start: 0.8401 (m-80) cc_final: 0.7966 (m-80) REVERT: C 129 MET cc_start: 0.8006 (mtm) cc_final: 0.7593 (mtm) REVERT: C 148 ASN cc_start: 0.8165 (t0) cc_final: 0.7262 (t0) REVERT: C 155 TYR cc_start: 0.7491 (t80) cc_final: 0.6683 (t80) REVERT: C 209 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8428 (p) REVERT: C 248 ASP cc_start: 0.8363 (t0) cc_final: 0.8022 (m-30) REVERT: C 273 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8638 (p90) REVERT: C 345 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.6192 (p-80) REVERT: C 366 MET cc_start: 0.6846 (mtt) cc_final: 0.6571 (mmt) REVERT: D 17 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8348 (tp) REVERT: D 40 CYS cc_start: 0.7525 (m) cc_final: 0.7255 (m) REVERT: D 82 MET cc_start: 0.8485 (mmm) cc_final: 0.7622 (mmt) REVERT: D 160 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7022 (ttt) REVERT: D 211 MET cc_start: 0.8691 (tpt) cc_final: 0.8408 (tpt) REVERT: E 37 TYR cc_start: 0.8018 (m-10) cc_final: 0.7744 (m-10) REVERT: E 81 ILE cc_start: 0.5426 (OUTLIER) cc_final: 0.5180 (pp) REVERT: E 118 ARG cc_start: 0.1657 (OUTLIER) cc_final: -0.3479 (ttt180) REVERT: F 100 ARG cc_start: 0.7571 (ttp80) cc_final: 0.7331 (ttp80) REVERT: G 43 ARG cc_start: 0.7416 (tpt170) cc_final: 0.7119 (tpt170) REVERT: G 48 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7781 (mpp80) REVERT: H 53 ASP cc_start: 0.8752 (p0) cc_final: 0.7906 (p0) REVERT: I 1 MET cc_start: 0.5564 (OUTLIER) cc_final: 0.3827 (mmm) REVERT: I 2 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7884 (mp) REVERT: I 16 SER cc_start: 0.6404 (OUTLIER) cc_final: 0.6078 (p) REVERT: J 33 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8407 (pt0) REVERT: J 45 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: N 307 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7183 (t80) REVERT: O 120 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.6985 (mpp) REVERT: O 238 LYS cc_start: 0.7533 (mtmm) cc_final: 0.7263 (mtmm) REVERT: O 326 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8664 (t) REVERT: O 437 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7490 (p0) REVERT: O 438 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: P 46 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8953 (mm) REVERT: P 102 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8424 (mm) REVERT: P 202 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8331 (pp20) REVERT: P 216 ASP cc_start: 0.7943 (t70) cc_final: 0.7681 (t70) REVERT: P 331 ASP cc_start: 0.7990 (t0) cc_final: 0.7738 (t0) REVERT: P 345 HIS cc_start: 0.7037 (OUTLIER) cc_final: 0.5357 (p-80) REVERT: Q 4 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: Q 71 GLN cc_start: 0.8472 (tt0) cc_final: 0.7963 (tm-30) REVERT: R 12 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8157 (t0) REVERT: R 37 TYR cc_start: 0.7455 (m-80) cc_final: 0.7092 (m-80) REVERT: R 78 LEU cc_start: 0.7184 (pt) cc_final: 0.6480 (mp) REVERT: R 96 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6708 (pp) REVERT: R 136 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8404 (mm) REVERT: S 12 ARG cc_start: -0.1212 (OUTLIER) cc_final: -0.2727 (pmt-80) REVERT: S 33 MET cc_start: 0.8466 (mpp) cc_final: 0.7929 (mpp) REVERT: S 108 TRP cc_start: 0.7312 (t-100) cc_final: 0.7041 (t-100) REVERT: T 3 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.5530 (ptm160) REVERT: T 71 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8476 (mtmt) REVERT: U 15 ASP cc_start: 0.7469 (t0) cc_final: 0.7180 (t70) REVERT: U 23 GLN cc_start: 0.8943 (tp-100) cc_final: 0.8485 (tp-100) REVERT: U 29 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7833 (mtmm) REVERT: U 34 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8177 (tpp80) REVERT: U 53 ASP cc_start: 0.8904 (p0) cc_final: 0.8432 (p0) REVERT: V 47 ARG cc_start: 0.5596 (ppt170) cc_final: 0.5273 (ppt170) REVERT: W 10 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8173 (tp) REVERT: W 45 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7404 (mp0) outliers start: 163 outliers final: 86 residues processed: 422 average time/residue: 1.3022 time to fit residues: 680.4643 Evaluate side-chains 393 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 275 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 GLU 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 A residue 383 LEU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 261 SER 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 407 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 172 LYS 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 273 TYR Chi-restraints excluded: chain C residue 310 SER 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 117 VAL 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 81 ILE Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 147 ILE 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 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 I residue 30 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 38 TRP Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 127 ILE 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 255 ILE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 120 MET Chi-restraints excluded: chain O residue 186 VAL 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 372 VAL Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain O residue 437 ASP Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 46 LEU 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 202 GLU 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 310 SER 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 R residue 12 ASP Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 136 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 T residue 1 MET Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 17 TYR Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 10 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 57 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 405 optimal weight: 0.0370 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 overall best weight: 1.2062 ------------------------------------------------------------------------------- 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 240 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN G 80 ASN ** N 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.118976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.090369 restraints weight = 62114.554| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.59 r_work: 0.3166 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.7235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.587 34693 Z= 0.184 Angle : 0.677 18.023 47173 Z= 0.329 Chirality : 0.045 0.357 5168 Planarity : 0.005 0.101 6040 Dihedral : 6.689 87.272 4743 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.34 % Favored : 94.36 % Rotamer: Outliers : 4.79 % Allowed : 28.75 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 4234 helix: 1.25 (0.11), residues: 2052 sheet: -0.19 (0.27), residues: 390 loop : -1.07 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP P 163 HIS 0.008 0.001 HIS A 328 PHE 0.028 0.002 PHE A 336 TYR 0.024 0.002 TYR B 168 ARG 0.016 0.001 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 1722) hydrogen bonds : angle 4.66833 ( 4935) metal coordination : bond 0.00999 ( 8) metal coordination : angle 10.63600 ( 7) SS BOND : bond 0.00637 ( 5) SS BOND : angle 1.49963 ( 10) covalent geometry : bond 0.00435 (34674) covalent geometry : angle 0.66431 (47156) Misc. bond : bond 0.27075 ( 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 462 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 290 time to evaluate : 4.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.7969 (t) REVERT: A 351 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: B 120 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7908 (mtt) REVERT: B 376 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7501 (tp30) REVERT: C 57 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8554 (m) REVERT: C 75 TYR cc_start: 0.8457 (m-80) cc_final: 0.8024 (m-80) REVERT: C 129 MET cc_start: 0.8311 (mtm) cc_final: 0.8065 (mtm) REVERT: C 148 ASN cc_start: 0.8203 (t0) cc_final: 0.7337 (t0) REVERT: C 155 TYR cc_start: 0.7450 (t80) cc_final: 0.6739 (t80) REVERT: C 209 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8399 (p) REVERT: C 248 ASP cc_start: 0.8382 (t0) cc_final: 0.7999 (m-30) REVERT: C 345 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.5838 (p-80) REVERT: C 366 MET cc_start: 0.7014 (mtt) cc_final: 0.6745 (mmt) REVERT: D 17 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8379 (tp) REVERT: D 40 CYS cc_start: 0.7491 (m) cc_final: 0.7242 (m) REVERT: D 82 MET cc_start: 0.8445 (mmm) cc_final: 0.7439 (mmt) REVERT: D 160 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.6636 (ttt) REVERT: D 211 MET cc_start: 0.8781 (tpt) cc_final: 0.8564 (tpt) REVERT: E 37 TYR cc_start: 0.7884 (m-10) cc_final: 0.7636 (m-10) REVERT: G 48 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7958 (mpp80) REVERT: H 47 ARG cc_start: 0.8071 (mmm-85) cc_final: 0.7689 (mmm-85) REVERT: H 53 ASP cc_start: 0.8831 (p0) cc_final: 0.7962 (p0) REVERT: I 1 MET cc_start: 0.5873 (OUTLIER) cc_final: 0.4240 (mmm) REVERT: I 2 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7983 (mt) REVERT: J 10 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7618 (tp) REVERT: J 33 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8446 (pt0) REVERT: J 45 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: N 172 GLU cc_start: 0.7270 (mp0) cc_final: 0.6917 (pm20) REVERT: N 176 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8762 (mmtt) REVERT: N 307 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7270 (t80) REVERT: O 120 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7142 (mpp) REVERT: O 326 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8577 (t) REVERT: O 438 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: O 439 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6780 (pp) REVERT: P 46 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8966 (mm) REVERT: P 49 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8912 (tp) REVERT: P 82 MET cc_start: 0.7452 (mtm) cc_final: 0.7230 (ptp) REVERT: P 202 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8370 (pp20) REVERT: P 216 ASP cc_start: 0.8244 (t70) cc_final: 0.8007 (t70) REVERT: P 331 ASP cc_start: 0.8109 (t0) cc_final: 0.7875 (t0) REVERT: P 345 HIS cc_start: 0.7002 (OUTLIER) cc_final: 0.5069 (p-80) REVERT: R 12 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8109 (t0) REVERT: R 37 TYR cc_start: 0.7378 (m-80) cc_final: 0.6938 (m-80) REVERT: R 78 LEU cc_start: 0.7434 (pt) cc_final: 0.6852 (mp) REVERT: R 96 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6601 (pp) REVERT: S 12 ARG cc_start: -0.1162 (OUTLIER) cc_final: -0.2453 (pmt-80) REVERT: S 33 MET cc_start: 0.8489 (mpp) cc_final: 0.7948 (mpp) REVERT: T 3 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.5429 (ptm160) REVERT: T 71 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8471 (mtmt) REVERT: U 15 ASP cc_start: 0.7496 (t0) cc_final: 0.7204 (t70) REVERT: U 23 GLN cc_start: 0.9022 (tp-100) cc_final: 0.8594 (tp-100) REVERT: U 34 ARG cc_start: 0.8495 (tpp80) cc_final: 0.8169 (tpt-90) REVERT: U 53 ASP cc_start: 0.8902 (p0) cc_final: 0.8460 (p0) REVERT: W 45 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: X 1 MET cc_start: 0.3282 (OUTLIER) cc_final: 0.2417 (ptt) REVERT: X 39 ARG cc_start: 0.5413 (pmt170) cc_final: 0.4096 (mpp-170) outliers start: 172 outliers final: 90 residues processed: 422 average time/residue: 1.2786 time to fit residues: 670.3838 Evaluate side-chains 392 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 273 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 149 VAL 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 351 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 261 SER 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 407 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 8 HIS 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 310 SER 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 25 SER Chi-restraints excluded: chain D residue 117 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 147 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 165 TYR 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 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 1 MET 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 30 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 N residue 99 ILE 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 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 8 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 89 ILE 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 326 THR Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain O residue 439 LEU Chi-restraints excluded: chain P residue 39 ILE 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 172 LYS Chi-restraints excluded: chain P residue 202 GLU Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 310 SER Chi-restraints excluded: chain P residue 345 HIS Chi-restraints excluded: chain Q residue 212 MET Chi-restraints excluded: chain R residue 12 ASP Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 98 VAL 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 R residue 193 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 1 MET Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 17 TYR 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 22 VAL Chi-restraints excluded: chain W residue 7 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 93 optimal weight: 0.9980 chunk 337 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 171 optimal weight: 0.5980 chunk 300 optimal weight: 0.8980 chunk 65 optimal weight: 0.2980 chunk 197 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 357 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B 240 HIS ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN N 430 GLN Q 71 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.120028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.091410 restraints weight = 62106.768| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.62 r_work: 0.3185 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.7323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.540 34693 Z= 0.142 Angle : 0.653 16.896 47173 Z= 0.315 Chirality : 0.043 0.349 5168 Planarity : 0.004 0.100 6040 Dihedral : 6.605 87.627 4743 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.84 % Favored : 94.85 % Rotamer: Outliers : 3.93 % Allowed : 29.81 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.13), residues: 4234 helix: 1.37 (0.11), residues: 2041 sheet: -0.11 (0.27), residues: 386 loop : -1.05 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 443 HIS 0.007 0.001 HIS A 328 PHE 0.016 0.001 PHE B 26 TYR 0.017 0.001 TYR A 434 ARG 0.013 0.000 ARG H 36 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 1722) hydrogen bonds : angle 4.60265 ( 4935) metal coordination : bond 0.00943 ( 8) metal coordination : angle 10.38943 ( 7) SS BOND : bond 0.00444 ( 5) SS BOND : angle 1.34867 ( 10) covalent geometry : bond 0.00338 (34674) covalent geometry : angle 0.64054 (47156) Misc. bond : bond 0.24737 ( 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 424 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 283 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.7964 (t) REVERT: A 351 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7414 (mm-30) REVERT: B 120 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7898 (mtt) REVERT: B 238 LYS cc_start: 0.7479 (ptpp) cc_final: 0.6989 (mtmt) REVERT: B 376 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7475 (tp30) REVERT: C 75 TYR cc_start: 0.8431 (m-80) cc_final: 0.7925 (m-80) REVERT: C 129 MET cc_start: 0.8295 (mtm) cc_final: 0.8087 (mtm) REVERT: C 148 ASN cc_start: 0.8162 (t0) cc_final: 0.7319 (t0) REVERT: C 155 TYR cc_start: 0.7517 (t80) cc_final: 0.6769 (t80) REVERT: C 209 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8503 (p) REVERT: C 248 ASP cc_start: 0.8374 (t0) cc_final: 0.8090 (p0) REVERT: C 345 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.5976 (p-80) REVERT: C 366 MET cc_start: 0.6992 (mtt) cc_final: 0.6768 (mmt) REVERT: D 40 CYS cc_start: 0.7402 (m) cc_final: 0.7163 (m) REVERT: D 82 MET cc_start: 0.8381 (mmm) cc_final: 0.7334 (mmt) REVERT: D 160 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.6758 (ttt) REVERT: D 179 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7531 (tpt) REVERT: D 211 MET cc_start: 0.8714 (tpt) cc_final: 0.8376 (tpt) REVERT: E 37 TYR cc_start: 0.7874 (m-10) cc_final: 0.7625 (m-10) REVERT: E 81 ILE cc_start: 0.6186 (OUTLIER) cc_final: 0.5601 (tt) REVERT: G 48 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7937 (mpp80) REVERT: H 53 ASP cc_start: 0.8857 (p0) cc_final: 0.8001 (p0) REVERT: I 1 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.4288 (mmm) REVERT: I 2 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7960 (mt) REVERT: J 10 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7606 (tp) REVERT: J 33 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8432 (pt0) REVERT: J 45 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: K 16 ASN cc_start: 0.5383 (m-40) cc_final: 0.5148 (m-40) REVERT: N 172 GLU cc_start: 0.7297 (mp0) cc_final: 0.6926 (pm20) REVERT: N 176 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8820 (mmtt) REVERT: N 220 SER cc_start: 0.8846 (t) cc_final: 0.8620 (p) REVERT: N 307 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7229 (t80) REVERT: O 120 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7144 (mpp) REVERT: O 238 LYS cc_start: 0.7655 (mtmm) cc_final: 0.7374 (pttm) REVERT: O 326 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8583 (t) REVERT: O 438 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: O 439 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6800 (pp) REVERT: P 46 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8970 (mm) REVERT: P 49 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8929 (tp) REVERT: P 202 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8347 (pp20) REVERT: P 216 ASP cc_start: 0.8193 (t70) cc_final: 0.7944 (t70) REVERT: P 331 ASP cc_start: 0.8077 (t0) cc_final: 0.7835 (t0) REVERT: P 345 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.5160 (p-80) REVERT: Q 142 SER cc_start: 0.8366 (m) cc_final: 0.7955 (p) REVERT: R 37 TYR cc_start: 0.7407 (m-80) cc_final: 0.7063 (m-80) REVERT: R 78 LEU cc_start: 0.7418 (pt) cc_final: 0.6854 (mp) REVERT: R 96 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6779 (pp) REVERT: S 12 ARG cc_start: -0.1044 (OUTLIER) cc_final: -0.2378 (pmt-80) REVERT: S 33 MET cc_start: 0.8470 (mpp) cc_final: 0.7978 (mpp) REVERT: T 1 MET cc_start: 0.1534 (OUTLIER) cc_final: 0.1146 (mpt) REVERT: T 3 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.5511 (ptm160) REVERT: T 66 GLU cc_start: 0.8762 (tp30) cc_final: 0.8500 (tp30) REVERT: T 71 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8431 (mtmt) REVERT: U 15 ASP cc_start: 0.7452 (t0) cc_final: 0.7142 (t70) REVERT: U 23 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8637 (tp-100) REVERT: U 34 ARG cc_start: 0.8541 (tpp80) cc_final: 0.8187 (tpt-90) REVERT: U 53 ASP cc_start: 0.8902 (p0) cc_final: 0.8465 (p0) REVERT: W 1 MET cc_start: 0.2742 (tpp) cc_final: 0.1727 (tpp) REVERT: W 45 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: X 1 MET cc_start: 0.3221 (OUTLIER) cc_final: 0.2518 (ptt) REVERT: X 39 ARG cc_start: 0.5497 (pmt170) cc_final: 0.4139 (mpp-170) outliers start: 141 outliers final: 86 residues processed: 395 average time/residue: 1.3556 time to fit residues: 664.5534 Evaluate side-chains 382 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 268 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 149 VAL 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 345 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 261 SER 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 407 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 8 HIS 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 310 SER Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 179 MET 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 133 VAL 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 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 18 THR Chi-restraints excluded: chain I residue 30 VAL 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 N residue 99 ILE Chi-restraints excluded: chain N residue 167 VAL 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 309 THR 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 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 326 THR Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 407 ASP Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain O residue 439 LEU Chi-restraints excluded: chain P residue 39 ILE 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 60 THR Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 171 ASP Chi-restraints excluded: chain P residue 172 LYS Chi-restraints excluded: chain P residue 202 GLU Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 310 SER 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 98 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 193 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 1 MET Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 17 TYR 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 22 VAL Chi-restraints excluded: chain W residue 7 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 66 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 397 optimal weight: 0.6980 chunk 352 optimal weight: 0.6980 chunk 378 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 381 optimal weight: 1.9990 chunk 344 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 124 optimal weight: 0.0060 chunk 369 optimal weight: 0.0570 overall best weight: 0.4514 ------------------------------------------------------------------------------- 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** B 143 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 GLN Q 71 GLN U 63 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.121263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.092925 restraints weight = 61860.925| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.62 r_work: 0.3215 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.7430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.499 34693 Z= 0.124 Angle : 0.639 15.846 47173 Z= 0.308 Chirality : 0.043 0.336 5168 Planarity : 0.004 0.100 6040 Dihedral : 6.471 87.646 4742 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.72 % Favored : 94.97 % Rotamer: Outliers : 3.43 % Allowed : 30.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.13), residues: 4234 helix: 1.48 (0.11), residues: 2048 sheet: -0.01 (0.28), residues: 373 loop : -0.98 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 443 HIS 0.007 0.001 HIS A 328 PHE 0.024 0.001 PHE A 336 TYR 0.018 0.001 TYR C 224 ARG 0.007 0.000 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 1722) hydrogen bonds : angle 4.50338 ( 4935) metal coordination : bond 0.00933 ( 8) metal coordination : angle 9.54782 ( 7) SS BOND : bond 0.00427 ( 5) SS BOND : angle 1.28985 ( 10) covalent geometry : bond 0.00291 (34674) covalent geometry : angle 0.62789 (47156) Misc. bond : bond 0.22604 ( 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 418 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 295 time to evaluate : 4.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.7953 (t) REVERT: A 351 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7382 (mm-30) REVERT: B 4 VAL cc_start: 0.3518 (OUTLIER) cc_final: 0.3276 (m) REVERT: B 120 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7850 (mtt) REVERT: B 238 LYS cc_start: 0.7446 (ptpp) cc_final: 0.6942 (mtmt) REVERT: C 75 TYR cc_start: 0.8424 (m-80) cc_final: 0.7927 (m-80) REVERT: C 129 MET cc_start: 0.8348 (mtm) cc_final: 0.7813 (mtp) REVERT: C 148 ASN cc_start: 0.8209 (t0) cc_final: 0.7254 (t0) REVERT: C 155 TYR cc_start: 0.7453 (t80) cc_final: 0.6701 (t80) REVERT: C 209 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8482 (p) REVERT: C 248 ASP cc_start: 0.8250 (t0) cc_final: 0.7967 (p0) REVERT: C 345 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.6422 (p-80) REVERT: C 366 MET cc_start: 0.6959 (mtt) cc_final: 0.6709 (mmt) REVERT: D 31 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7440 (mt0) REVERT: D 40 CYS cc_start: 0.7349 (m) cc_final: 0.7119 (m) REVERT: D 82 MET cc_start: 0.8382 (mmm) cc_final: 0.7355 (mmt) REVERT: D 160 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.6927 (ttt) REVERT: D 179 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7674 (tpt) REVERT: D 211 MET cc_start: 0.8666 (tpt) cc_final: 0.8403 (tpt) REVERT: E 81 ILE cc_start: 0.6229 (OUTLIER) cc_final: 0.5566 (tt) REVERT: G 48 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7947 (mpp80) REVERT: H 53 ASP cc_start: 0.8862 (p0) cc_final: 0.8036 (p0) REVERT: I 1 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.4308 (mmm) REVERT: I 11 PHE cc_start: 0.6871 (m-80) cc_final: 0.6631 (m-10) REVERT: J 33 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8448 (pt0) REVERT: J 41 ASP cc_start: 0.8063 (m-30) cc_final: 0.7835 (m-30) REVERT: J 45 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: K 16 ASN cc_start: 0.5203 (m-40) cc_final: 0.4945 (m-40) REVERT: N 172 GLU cc_start: 0.7304 (mp0) cc_final: 0.6943 (pm20) REVERT: N 220 SER cc_start: 0.8882 (t) cc_final: 0.8495 (p) REVERT: N 307 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7311 (t80) REVERT: O 120 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7630 (mtt) REVERT: O 438 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: O 439 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6849 (pp) REVERT: P 49 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8922 (tp) REVERT: P 202 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8349 (pp20) REVERT: P 216 ASP cc_start: 0.8134 (t70) cc_final: 0.7876 (t70) REVERT: P 331 ASP cc_start: 0.8037 (t0) cc_final: 0.7810 (t0) REVERT: P 345 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.5553 (p-80) REVERT: Q 142 SER cc_start: 0.8288 (m) cc_final: 0.7869 (p) REVERT: R 37 TYR cc_start: 0.7373 (m-80) cc_final: 0.7071 (m-80) REVERT: R 96 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6865 (pp) REVERT: R 192 MET cc_start: 0.5617 (mmm) cc_final: 0.5370 (tmt) REVERT: S 12 ARG cc_start: -0.1011 (OUTLIER) cc_final: -0.2517 (pmt-80) REVERT: S 33 MET cc_start: 0.8454 (mpp) cc_final: 0.7834 (mpp) REVERT: T 1 MET cc_start: 0.1590 (OUTLIER) cc_final: 0.1132 (mpt) REVERT: T 3 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.5632 (ptm160) REVERT: T 66 GLU cc_start: 0.8749 (tp30) cc_final: 0.8472 (tp30) REVERT: U 15 ASP cc_start: 0.7434 (t0) cc_final: 0.7133 (t70) REVERT: U 23 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8596 (tp-100) REVERT: U 34 ARG cc_start: 0.8540 (tpp80) cc_final: 0.8192 (tpt-90) REVERT: U 53 ASP cc_start: 0.8891 (p0) cc_final: 0.8460 (p0) REVERT: W 1 MET cc_start: 0.3322 (tpp) cc_final: 0.2474 (mmm) REVERT: W 45 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: X 39 ARG cc_start: 0.5497 (pmt170) cc_final: 0.4140 (mpp-170) outliers start: 123 outliers final: 77 residues processed: 388 average time/residue: 1.4517 time to fit residues: 700.3546 Evaluate side-chains 386 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 285 time to evaluate : 4.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 VAL 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 345 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 261 SER 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 407 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 8 HIS 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 345 HIS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 179 MET 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 133 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 193 VAL 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 H residue 24 CYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 30 VAL 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 38 TRP Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 240 GLN 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 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 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 O residue 438 GLU Chi-restraints excluded: chain O residue 439 LEU Chi-restraints excluded: chain P residue 39 ILE 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 162 GLU Chi-restraints excluded: chain P residue 172 LYS Chi-restraints excluded: chain P residue 202 GLU Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 345 HIS Chi-restraints excluded: chain Q residue 164 ILE 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 98 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 193 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 1 MET Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 17 TYR Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 7 THR 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 296 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 395 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 381 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 372 optimal weight: 10.0000 chunk 355 optimal weight: 7.9990 chunk 328 optimal weight: 2.9990 chunk 342 optimal weight: 0.0000 chunk 106 optimal weight: 0.0270 overall best weight: 1.1446 ------------------------------------------------------------------------------- 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** ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 HIS ** N 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 GLN Q 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.119239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.090737 restraints weight = 61968.821| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.60 r_work: 0.3174 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.7552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.573 34693 Z= 0.175 Angle : 0.674 16.332 47173 Z= 0.327 Chirality : 0.044 0.379 5168 Planarity : 0.005 0.099 6040 Dihedral : 6.539 88.443 4742 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.01 % Favored : 94.69 % Rotamer: Outliers : 3.45 % Allowed : 30.19 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.13), residues: 4234 helix: 1.34 (0.11), residues: 2057 sheet: -0.12 (0.27), residues: 386 loop : -1.04 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 443 HIS 0.010 0.001 HIS A 328 PHE 0.017 0.002 PHE C 91 TYR 0.020 0.001 TYR P 81 ARG 0.015 0.001 ARG K 39 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 1722) hydrogen bonds : angle 4.57964 ( 4935) metal coordination : bond 0.00916 ( 8) metal coordination : angle 9.82211 ( 7) SS BOND : bond 0.00456 ( 5) SS BOND : angle 1.31591 ( 10) covalent geometry : bond 0.00420 (34674) covalent geometry : angle 0.66352 (47156) Misc. bond : bond 0.25999 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21534.17 seconds wall clock time: 375 minutes 50.85 seconds (22550.85 seconds total)