Starting phenix.real_space_refine on Sat Jun 21 18:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7trj_26098/06_2025/7trj_26098.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trj_26098/06_2025/7trj_26098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7trj_26098/06_2025/7trj_26098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trj_26098/06_2025/7trj_26098.map" model { file = "/net/cci-nas-00/data/ceres_data/7trj_26098/06_2025/7trj_26098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trj_26098/06_2025/7trj_26098.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 16062 2.51 5 N 4372 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25190 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3210 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "G" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2203 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1861 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2571 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: B, D, H, J, F Time building chain proxies: 19.39, per 1000 atoms: 0.77 Number of scatterers: 25190 At special positions: 0 Unit cell: (141.95, 132.765, 166.165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 142 16.00 O 4614 8.00 N 4372 7.00 C 16062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" O GLU D 293 " - pdb=" N VAL D 294 " distance=2.25 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.89 Conformation dependent library (CDL) restraints added in 3.7 seconds 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6144 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 32 sheets defined 45.8% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.726A pdb=" N ASP A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.670A pdb=" N LEU A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.523A pdb=" N TYR A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.534A pdb=" N ILE A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.699A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.751A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.574A pdb=" N ALA A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.518A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 4.273A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 128 through 153 removed outlier: 3.586A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.722A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.564A pdb=" N LYS D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.813A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.680A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.611A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 removed outlier: 3.827A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 196' Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 240 Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.441A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 Processing helix chain 'E' and resid 312 through 324 Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'E' and resid 368 through 380 removed outlier: 4.085A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 420 through 430 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 459 through 464 Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 508 through 510 No H-bonds generated for 'chain 'E' and resid 508 through 510' Processing helix chain 'E' and resid 511 through 519 removed outlier: 3.556A pdb=" N VAL E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS E 519 " --> pdb=" O VAL E 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 17 removed outlier: 4.204A pdb=" N ASP G 17 " --> pdb=" O GLN G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.585A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 60 Processing helix chain 'G' and resid 62 through 81 removed outlier: 3.868A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 106 removed outlier: 3.626A pdb=" N LEU G 106 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 179 through 183 removed outlier: 4.047A pdb=" N VAL G 183 " --> pdb=" O ASP G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 231 through 235 removed outlier: 3.850A pdb=" N LYS G 234 " --> pdb=" O GLU G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.516A pdb=" N LYS G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 294 through 304 removed outlier: 3.588A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 33 Processing helix chain 'I' and resid 34 through 35 No H-bonds generated for 'chain 'I' and resid 34 through 35' Processing helix chain 'I' and resid 36 through 44 removed outlier: 3.539A pdb=" N LEU I 40 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 93 Processing helix chain 'I' and resid 114 through 124 removed outlier: 4.169A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 209 through 218 Processing helix chain 'I' and resid 223 through 236 removed outlier: 5.366A pdb=" N ILE I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Proline residue: I 230 - end of helix Processing helix chain 'I' and resid 262 through 266 Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix removed outlier: 3.741A pdb=" N ALA I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.726A pdb=" N ASP B 62 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.670A pdb=" N LEU B 67 " --> pdb=" O PRO B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.523A pdb=" N TYR B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.534A pdb=" N ILE B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.699A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.752A pdb=" N PHE B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.574A pdb=" N ALA B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.518A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 4.273A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 128 through 153 removed outlier: 3.586A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 180 Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.722A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.565A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.813A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.680A pdb=" N LEU C 320 " --> pdb=" O PRO C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.611A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 3.827A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET F 196 " --> pdb=" O THR F 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 196' Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 240 Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.441A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 Processing helix chain 'F' and resid 312 through 324 Processing helix chain 'F' and resid 339 through 352 Processing helix chain 'F' and resid 368 through 380 removed outlier: 4.086A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 459 through 464 Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 508 through 510 No H-bonds generated for 'chain 'F' and resid 508 through 510' Processing helix chain 'F' and resid 511 through 519 removed outlier: 3.555A pdb=" N VAL F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS F 519 " --> pdb=" O VAL F 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 17 removed outlier: 4.205A pdb=" N ASP H 17 " --> pdb=" O GLN H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 35 removed outlier: 3.584A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 60 Processing helix chain 'H' and resid 62 through 81 removed outlier: 3.867A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 106 removed outlier: 3.626A pdb=" N LEU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 179 through 183 removed outlier: 4.047A pdb=" N VAL H 183 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 222 Processing helix chain 'H' and resid 231 through 235 removed outlier: 3.849A pdb=" N LYS H 234 " --> pdb=" O GLU H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.515A pdb=" N LYS H 251 " --> pdb=" O PRO H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 294 through 304 removed outlier: 3.588A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 Processing helix chain 'J' and resid 34 through 35 No H-bonds generated for 'chain 'J' and resid 34 through 35' Processing helix chain 'J' and resid 36 through 44 removed outlier: 3.539A pdb=" N LEU J 40 " --> pdb=" O ILE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 93 Processing helix chain 'J' and resid 114 through 124 removed outlier: 4.169A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 209 through 218 Processing helix chain 'J' and resid 223 through 236 removed outlier: 5.365A pdb=" N ILE J 229 " --> pdb=" O ARG J 225 " (cutoff:3.500A) Proline residue: J 230 - end of helix Processing helix chain 'J' and resid 262 through 266 Processing helix chain 'J' and resid 315 through 334 Proline residue: J 327 - end of helix removed outlier: 3.741A pdb=" N ALA J 332 " --> pdb=" O LYS J 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.673A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS A 247 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LYS A 186 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE A 249 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N MET A 181 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N HIS A 290 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET A 183 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR A 292 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 185 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 212 through 217 removed outlier: 6.623A pdb=" N VAL A 212 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP A 206 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 227 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338 removed outlier: 3.544A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.423A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.339A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 401 through 402 removed outlier: 6.785A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 430 through 431 removed outlier: 6.797A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 329 through 331 removed outlier: 3.732A pdb=" N SER D 326 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 163 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE D 190 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR D 214 " --> pdb=" O ARG E 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.761A pdb=" N THR D 238 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.279A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR E 336 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLY E 404 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'G' and resid 175 through 178 removed outlier: 6.459A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AB7, first strand: chain 'I' and resid 73 through 77 removed outlier: 6.546A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER I 105 " --> pdb=" O HIS I 203 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N HIS I 203 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA I 202 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU I 131 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU I 204 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA I 129 " --> pdb=" O LEU I 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 119 through 124 removed outlier: 6.673A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS B 247 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LYS B 186 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE B 249 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N MET B 181 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N HIS B 290 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET B 183 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR B 292 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B 185 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AC1, first strand: chain 'B' and resid 212 through 217 removed outlier: 6.624A pdb=" N VAL B 212 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP B 206 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AC3, first strand: chain 'B' and resid 336 through 338 removed outlier: 3.544A pdb=" N ILE B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.423A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.339A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 401 through 402 removed outlier: 6.786A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 430 through 431 removed outlier: 6.797A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 329 through 331 removed outlier: 3.732A pdb=" N SER C 326 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU C 163 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE C 190 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR C 214 " --> pdb=" O ARG F 483 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.762A pdb=" N THR C 238 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 307 through 308 removed outlier: 6.321A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR F 336 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLY F 404 " --> pdb=" O TYR F 336 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AD3, first strand: chain 'H' and resid 175 through 178 removed outlier: 6.458A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AD5, first strand: chain 'J' and resid 73 through 77 removed outlier: 6.546A pdb=" N GLN J 4 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU J 104 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL J 6 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER J 105 " --> pdb=" O HIS J 203 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N HIS J 203 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA J 202 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU J 131 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU J 204 " --> pdb=" O ALA J 129 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA J 129 " --> pdb=" O LEU J 204 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3039 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: 10.59 Time building geometry restraints manager: 8.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8288 1.35 - 1.47: 5617 1.47 - 1.59: 11533 1.59 - 1.71: 0 1.71 - 1.84: 216 Bond restraints: 25654 Sorted by residual: bond pdb=" CA ILE J 229 " pdb=" CB ILE J 229 " ideal model delta sigma weight residual 1.539 1.497 0.042 5.40e-03 3.43e+04 5.94e+01 bond pdb=" CA ILE I 229 " pdb=" CB ILE I 229 " ideal model delta sigma weight residual 1.539 1.498 0.041 5.40e-03 3.43e+04 5.80e+01 bond pdb=" CA SER F 510 " pdb=" C SER F 510 " ideal model delta sigma weight residual 1.525 1.505 0.020 1.38e-02 5.25e+03 2.15e+00 bond pdb=" CA SER E 510 " pdb=" C SER E 510 " ideal model delta sigma weight residual 1.525 1.505 0.020 1.38e-02 5.25e+03 2.07e+00 bond pdb=" C VAL I 326 " pdb=" N PRO I 327 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.51e-02 4.39e+03 1.88e+00 ... (remaining 25649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 33920 2.26 - 4.51: 683 4.51 - 6.77: 125 6.77 - 9.03: 24 9.03 - 11.29: 20 Bond angle restraints: 34772 Sorted by residual: angle pdb=" CA LYS J 328 " pdb=" CB LYS J 328 " pdb=" CG LYS J 328 " ideal model delta sigma weight residual 114.10 125.16 -11.06 2.00e+00 2.50e-01 3.06e+01 angle pdb=" CA LYS I 328 " pdb=" CB LYS I 328 " pdb=" CG LYS I 328 " ideal model delta sigma weight residual 114.10 125.15 -11.05 2.00e+00 2.50e-01 3.05e+01 angle pdb=" N PHE B 56 " pdb=" CA PHE B 56 " pdb=" C PHE B 56 " ideal model delta sigma weight residual 110.70 102.65 8.05 1.55e+00 4.16e-01 2.69e+01 angle pdb=" N PHE A 56 " pdb=" CA PHE A 56 " pdb=" C PHE A 56 " ideal model delta sigma weight residual 110.70 102.71 7.99 1.55e+00 4.16e-01 2.66e+01 angle pdb=" C LYS H 15 " pdb=" N GLU H 16 " pdb=" CA GLU H 16 " ideal model delta sigma weight residual 120.44 114.04 6.40 1.30e+00 5.92e-01 2.42e+01 ... (remaining 34767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 14010 17.41 - 34.83: 1033 34.83 - 52.24: 342 52.24 - 69.66: 170 69.66 - 87.07: 44 Dihedral angle restraints: 15599 sinusoidal: 6155 harmonic: 9444 Sorted by residual: dihedral pdb=" CB GLU D 293 " pdb=" O GLU D 293 " pdb=" N VAL D 294 " pdb=" CB VAL D 294 " ideal model delta sinusoidal sigma weight residual -86.00 -135.04 49.04 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CA ASP A 139 " pdb=" CB ASP A 139 " pdb=" CG ASP A 139 " pdb=" OD1 ASP A 139 " ideal model delta sinusoidal sigma weight residual -30.00 -86.26 56.26 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP B 139 " pdb=" CB ASP B 139 " pdb=" CG ASP B 139 " pdb=" OD1 ASP B 139 " ideal model delta sinusoidal sigma weight residual -30.00 -86.22 56.22 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 15596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3179 0.056 - 0.111: 751 0.111 - 0.167: 163 0.167 - 0.222: 5 0.222 - 0.278: 6 Chirality restraints: 4104 Sorted by residual: chirality pdb=" CA GLN J 325 " pdb=" N GLN J 325 " pdb=" C GLN J 325 " pdb=" CB GLN J 325 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA GLN I 325 " pdb=" N GLN I 325 " pdb=" C GLN I 325 " pdb=" CB GLN I 325 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA LYS H 15 " pdb=" N LYS H 15 " pdb=" C LYS H 15 " pdb=" CB LYS H 15 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 4101 not shown) Planarity restraints: 4414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 509 " -0.028 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C CYS E 509 " 0.095 2.00e-02 2.50e+03 pdb=" O CYS E 509 " -0.035 2.00e-02 2.50e+03 pdb=" N SER E 510 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 509 " 0.028 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C CYS F 509 " -0.094 2.00e-02 2.50e+03 pdb=" O CYS F 509 " 0.035 2.00e-02 2.50e+03 pdb=" N SER F 510 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 104 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU B 104 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU B 104 " -0.024 2.00e-02 2.50e+03 pdb=" N HIS B 105 " -0.022 2.00e-02 2.50e+03 ... (remaining 4411 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 398 2.64 - 3.21: 22661 3.21 - 3.77: 38435 3.77 - 4.34: 53319 4.34 - 4.90: 89533 Nonbonded interactions: 204346 Sorted by model distance: nonbonded pdb=" OD1 ASP A 271 " pdb=" NH2 ARG A 274 " model vdw 2.080 3.120 nonbonded pdb=" OD1 ASP B 271 " pdb=" NH2 ARG B 274 " model vdw 2.082 3.120 nonbonded pdb=" OG SER C 30 " pdb=" OE1 GLU C 33 " model vdw 2.142 3.040 nonbonded pdb=" OG SER D 30 " pdb=" OE1 GLU D 33 " model vdw 2.142 3.040 nonbonded pdb=" O TYR J 124 " pdb=" NH1 ARG J 299 " model vdw 2.180 3.120 ... (remaining 204341 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 4.160 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: 1.160 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 66.210 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.100 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.004 0.217 25655 Z= 0.190 Angle : 0.871 34.972 34774 Z= 0.488 Chirality : 0.050 0.278 4104 Planarity : 0.005 0.055 4414 Dihedral : 16.162 87.072 9452 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.62 % Favored : 96.25 % Rotamer: Outliers : 6.92 % Allowed : 13.45 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3174 helix: 0.03 (0.14), residues: 1282 sheet: -1.82 (0.21), residues: 452 loop : -2.12 (0.14), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 51 HIS 0.011 0.001 HIS A 304 PHE 0.020 0.001 PHE B 215 TYR 0.020 0.001 TYR B 306 ARG 0.035 0.001 ARG B 171 Details of bonding type rmsd hydrogen bonds : bond 0.16283 ( 1086) hydrogen bonds : angle 6.00812 ( 3039) SS BOND : bond 0.21712 ( 1) SS BOND : angle 28.86574 ( 2) covalent geometry : bond 0.00329 (25654) covalent geometry : angle 0.84341 (34772) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 517 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8928 (mm) REVERT: D 47 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8726 (p) REVERT: E 169 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8352 (t) REVERT: E 510 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8282 (p) REVERT: G 83 TYR cc_start: 0.4340 (OUTLIER) cc_final: 0.3894 (m-80) REVERT: G 90 LYS cc_start: 0.3665 (OUTLIER) cc_final: 0.3387 (ttpp) REVERT: G 93 MET cc_start: 0.6185 (ttm) cc_final: 0.5449 (ptm) REVERT: G 103 ARG cc_start: 0.7708 (tpp80) cc_final: 0.7463 (mtt180) REVERT: G 149 SER cc_start: 0.7690 (OUTLIER) cc_final: 0.7413 (t) REVERT: G 245 ASP cc_start: 0.7706 (t0) cc_final: 0.7447 (t0) REVERT: I 50 GLU cc_start: 0.8399 (tp30) cc_final: 0.8194 (tp30) REVERT: I 75 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8672 (mp) REVERT: I 116 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8378 (mm-30) REVERT: I 217 GLU cc_start: 0.8790 (tp30) cc_final: 0.8491 (tm-30) REVERT: I 227 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7828 (mt-10) REVERT: I 316 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8567 (tm) REVERT: B 98 LYS cc_start: 0.7687 (mttm) cc_final: 0.7404 (mttt) REVERT: B 150 LEU cc_start: 0.8681 (tp) cc_final: 0.8444 (tm) REVERT: B 166 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: B 355 ILE cc_start: 0.8302 (mt) cc_final: 0.7943 (mm) REVERT: B 401 ARG cc_start: 0.7127 (mtp-110) cc_final: 0.6707 (ptm160) REVERT: B 418 GLU cc_start: 0.8585 (tt0) cc_final: 0.8353 (tt0) REVERT: B 428 ARG cc_start: 0.7064 (mtm110) cc_final: 0.6693 (mmt180) REVERT: C 111 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7012 (ttmt) REVERT: F 173 TYR cc_start: 0.7362 (t80) cc_final: 0.6899 (t80) REVERT: F 198 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.6196 (mp) REVERT: F 251 ASP cc_start: 0.6412 (t70) cc_final: 0.6124 (t70) REVERT: H 14 MET cc_start: 0.8006 (mmm) cc_final: 0.7568 (tmt) REVERT: H 36 ARG cc_start: 0.5657 (mmt-90) cc_final: 0.5200 (mtm-85) REVERT: H 53 ILE cc_start: 0.8266 (pt) cc_final: 0.7980 (mt) REVERT: H 83 TYR cc_start: 0.4863 (OUTLIER) cc_final: 0.3908 (m-80) REVERT: H 92 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7646 (pp) REVERT: H 95 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: H 103 ARG cc_start: 0.8283 (tpp80) cc_final: 0.8050 (mtt180) REVERT: H 136 ARG cc_start: 0.7447 (tpt90) cc_final: 0.7119 (tmt170) REVERT: H 245 ASP cc_start: 0.8040 (t0) cc_final: 0.7625 (t0) REVERT: J 44 GLU cc_start: 0.8300 (tt0) cc_final: 0.8091 (pt0) REVERT: J 50 GLU cc_start: 0.7662 (tp30) cc_final: 0.7190 (tp30) REVERT: J 72 LYS cc_start: 0.8020 (mttp) cc_final: 0.7673 (tptp) REVERT: J 99 THR cc_start: 0.7406 (OUTLIER) cc_final: 0.7135 (p) REVERT: J 222 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7377 (t) REVERT: J 266 PHE cc_start: 0.7835 (m-80) cc_final: 0.7621 (m-10) REVERT: J 321 GLU cc_start: 0.8351 (tp30) cc_final: 0.8108 (tp30) outliers start: 192 outliers final: 44 residues processed: 658 average time/residue: 1.4702 time to fit residues: 1108.7189 Evaluate side-chains 338 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 277 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 90 LYS Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 222 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 7.9990 chunk 241 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 288 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 177 ASN A 214 HIS A 219 GLN A 286 GLN A 333 GLN A 341 ASN A 359 ASN A 371 ASN A 376 ASN D 80 ASN D 132 ASN D 188 HIS E 194 GLN E 213 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN E 455 ASN E 464 GLN G 48 ASN G 243 GLN I 323 ASN B 72 ASN B 197 HIS B 214 HIS B 219 GLN B 286 GLN B 359 ASN B 371 ASN C 80 ASN C 162 ASN C 188 HIS C 230 ASN F 189 GLN F 213 GLN F 265 GLN F 448 GLN F 455 ASN F 464 GLN H 48 ASN H 128 HIS H 222 GLN H 243 GLN J 323 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.116072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085491 restraints weight = 43791.013| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.58 r_work: 0.3160 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 25655 Z= 0.145 Angle : 0.589 16.462 34774 Z= 0.301 Chirality : 0.045 0.272 4104 Planarity : 0.004 0.045 4414 Dihedral : 6.488 86.050 3580 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.41 % Allowed : 18.93 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.52 (0.15), residues: 3174 helix: 1.09 (0.15), residues: 1298 sheet: -1.23 (0.23), residues: 442 loop : -1.38 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 51 HIS 0.006 0.001 HIS A 384 PHE 0.017 0.001 PHE C 272 TYR 0.017 0.001 TYR I 319 ARG 0.008 0.001 ARG G 28 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 1086) hydrogen bonds : angle 4.43800 ( 3039) SS BOND : bond 0.10919 ( 1) SS BOND : angle 11.89572 ( 2) covalent geometry : bond 0.00309 (25654) covalent geometry : angle 0.58244 (34772) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 294 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8559 (ttm110) cc_final: 0.8255 (mpt90) REVERT: A 418 GLU cc_start: 0.7872 (tt0) cc_final: 0.7403 (tp30) REVERT: A 450 SER cc_start: 0.8016 (t) cc_final: 0.7674 (t) REVERT: D 33 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8266 (tp30) REVERT: D 59 GLU cc_start: 0.8566 (tp30) cc_final: 0.8337 (tp30) REVERT: E 247 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7734 (mp0) REVERT: G 70 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7621 (mt-10) REVERT: G 93 MET cc_start: 0.6313 (ttm) cc_final: 0.5769 (ptm) REVERT: G 103 ARG cc_start: 0.7745 (tpp80) cc_final: 0.7453 (mtm-85) REVERT: G 120 LYS cc_start: 0.8224 (mttt) cc_final: 0.8011 (mmtt) REVERT: G 215 MET cc_start: 0.8880 (ttm) cc_final: 0.8674 (ttm) REVERT: G 245 ASP cc_start: 0.8328 (t0) cc_final: 0.7860 (t0) REVERT: I 217 GLU cc_start: 0.9010 (tp30) cc_final: 0.8700 (tm-30) REVERT: I 227 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8107 (mt-10) REVERT: I 316 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8334 (tm) REVERT: I 325 GLN cc_start: 0.9063 (mm110) cc_final: 0.8449 (mm-40) REVERT: B 53 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6495 (p0) REVERT: B 126 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: B 161 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8412 (mp) REVERT: B 166 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7364 (tp30) REVERT: B 355 ILE cc_start: 0.8097 (mt) cc_final: 0.7753 (mm) REVERT: B 357 GLU cc_start: 0.8381 (tt0) cc_final: 0.7963 (tt0) REVERT: B 418 GLU cc_start: 0.8634 (tt0) cc_final: 0.7757 (tp30) REVERT: B 428 ARG cc_start: 0.7160 (mtm110) cc_final: 0.6637 (mmt180) REVERT: C 172 ARG cc_start: 0.7800 (mmt180) cc_final: 0.7573 (mmt-90) REVERT: F 240 TYR cc_start: 0.8347 (t80) cc_final: 0.8054 (t80) REVERT: F 250 ARG cc_start: 0.7290 (ptp90) cc_final: 0.6988 (mtm-85) REVERT: H 14 MET cc_start: 0.8087 (mmm) cc_final: 0.7529 (tmt) REVERT: H 27 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7387 (mp) REVERT: H 48 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7842 (p0) REVERT: H 95 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7500 (pt0) REVERT: H 245 ASP cc_start: 0.8428 (t0) cc_final: 0.7851 (t0) REVERT: J 2 GLU cc_start: 0.7394 (tt0) cc_final: 0.7110 (tt0) REVERT: J 8 MET cc_start: 0.6549 (mpp) cc_final: 0.6331 (mpp) REVERT: J 37 TRP cc_start: 0.7232 (t60) cc_final: 0.6831 (t60) REVERT: J 72 LYS cc_start: 0.7836 (mttp) cc_final: 0.7590 (mppt) REVERT: J 99 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7445 (p) REVERT: J 194 ARG cc_start: 0.7439 (tpt90) cc_final: 0.7004 (tpt90) REVERT: J 199 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7311 (mt) REVERT: J 222 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7284 (p) REVERT: J 227 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7941 (mt-10) REVERT: J 309 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6217 (mp) REVERT: J 319 TYR cc_start: 0.8517 (t80) cc_final: 0.8195 (t80) REVERT: J 321 GLU cc_start: 0.8646 (tp30) cc_final: 0.8296 (tp30) REVERT: J 325 GLN cc_start: 0.9212 (mt0) cc_final: 0.8636 (tp-100) outliers start: 150 outliers final: 64 residues processed: 412 average time/residue: 1.3082 time to fit residues: 629.2554 Evaluate side-chains 321 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 245 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 222 THR Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 334 CYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 209 LYS Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 224 ILE Chi-restraints excluded: chain J residue 297 GLN Chi-restraints excluded: chain J residue 309 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 48 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 283 optimal weight: 0.0010 chunk 1 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 307 optimal weight: 10.0000 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 288 HIS A 333 GLN A 337 HIS A 359 ASN D 49 HIS D 230 ASN E 189 GLN G 128 HIS B 197 HIS B 359 ASN B 376 ASN C 49 HIS C 110 HIS H 48 ASN H 170 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.112974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081706 restraints weight = 43850.701| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.59 r_work: 0.3093 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 25655 Z= 0.147 Angle : 0.553 13.124 34774 Z= 0.283 Chirality : 0.044 0.240 4104 Planarity : 0.004 0.045 4414 Dihedral : 5.630 80.945 3527 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.12 % Allowed : 19.39 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.17 (0.15), residues: 3174 helix: 1.50 (0.15), residues: 1292 sheet: -0.66 (0.24), residues: 446 loop : -0.90 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 51 HIS 0.013 0.001 HIS H 170 PHE 0.022 0.001 PHE B 148 TYR 0.013 0.001 TYR I 38 ARG 0.011 0.001 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 1086) hydrogen bonds : angle 4.15698 ( 3039) SS BOND : bond 0.11240 ( 1) SS BOND : angle 9.28163 ( 2) covalent geometry : bond 0.00333 (25654) covalent geometry : angle 0.54893 (34772) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 264 time to evaluate : 3.379 Fit side-chains REVERT: A 121 ARG cc_start: 0.8752 (ttm110) cc_final: 0.8356 (mpt90) REVERT: D 33 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8423 (tp30) REVERT: D 59 GLU cc_start: 0.8707 (tp30) cc_final: 0.8428 (tp30) REVERT: D 217 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8218 (ptm) REVERT: E 247 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7928 (mp0) REVERT: E 415 MET cc_start: 0.8929 (tmm) cc_final: 0.8719 (ttm) REVERT: G 10 PHE cc_start: 0.6578 (t80) cc_final: 0.6374 (t80) REVERT: G 70 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7791 (mt-10) REVERT: G 103 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7491 (mtt180) REVERT: G 120 LYS cc_start: 0.8431 (mttt) cc_final: 0.8155 (mmtp) REVERT: G 121 ASP cc_start: 0.8417 (t0) cc_final: 0.8213 (t70) REVERT: G 149 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7727 (t) REVERT: G 245 ASP cc_start: 0.8553 (t0) cc_final: 0.8053 (t0) REVERT: I 316 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8385 (tm) REVERT: B 53 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6451 (p0) REVERT: B 126 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8263 (tp30) REVERT: B 161 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8411 (mp) REVERT: B 166 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7415 (tp30) REVERT: B 349 SER cc_start: 0.9093 (t) cc_final: 0.8891 (p) REVERT: B 355 ILE cc_start: 0.8154 (mt) cc_final: 0.7824 (mm) REVERT: B 418 GLU cc_start: 0.8572 (tt0) cc_final: 0.7729 (tp30) REVERT: B 428 ARG cc_start: 0.7330 (mtm110) cc_final: 0.6727 (mmt180) REVERT: C 48 ASP cc_start: 0.8245 (m-30) cc_final: 0.8024 (m-30) REVERT: C 63 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8252 (mtm110) REVERT: C 95 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7844 (mmp80) REVERT: C 172 ARG cc_start: 0.8081 (mmt180) cc_final: 0.7876 (mpt180) REVERT: C 319 GLU cc_start: 0.8624 (pt0) cc_final: 0.8366 (pm20) REVERT: F 194 GLN cc_start: 0.7406 (pt0) cc_final: 0.6934 (pt0) REVERT: F 195 PHE cc_start: 0.8376 (m-80) cc_final: 0.7820 (m-80) REVERT: F 250 ARG cc_start: 0.7375 (ptp90) cc_final: 0.7076 (mtm-85) REVERT: F 364 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8469 (mtp85) REVERT: F 458 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8772 (t0) REVERT: H 8 GLU cc_start: 0.8418 (mp0) cc_final: 0.8109 (pm20) REVERT: H 14 MET cc_start: 0.8188 (mmm) cc_final: 0.7561 (tmt) REVERT: H 95 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: H 245 ASP cc_start: 0.8626 (t0) cc_final: 0.8030 (t0) REVERT: J 2 GLU cc_start: 0.7449 (tt0) cc_final: 0.7124 (tt0) REVERT: J 37 TRP cc_start: 0.7259 (t60) cc_final: 0.6856 (t60) REVERT: J 44 GLU cc_start: 0.8639 (tp30) cc_final: 0.7958 (tp30) REVERT: J 50 GLU cc_start: 0.7423 (tp30) cc_final: 0.7196 (tp30) REVERT: J 72 LYS cc_start: 0.7903 (mttp) cc_final: 0.7654 (ttpp) REVERT: J 99 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7251 (p) REVERT: J 194 ARG cc_start: 0.7561 (tpt90) cc_final: 0.7282 (tpt90) REVERT: J 199 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7270 (mt) REVERT: J 222 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7493 (p) REVERT: J 309 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.5885 (mp) REVERT: J 321 GLU cc_start: 0.8668 (tp30) cc_final: 0.8369 (tp30) REVERT: J 325 GLN cc_start: 0.9248 (mt0) cc_final: 0.8733 (tp-100) outliers start: 142 outliers final: 66 residues processed: 376 average time/residue: 1.3032 time to fit residues: 574.7293 Evaluate side-chains 317 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 236 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 458 ASP Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 224 ILE Chi-restraints excluded: chain J residue 309 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 185 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 99 optimal weight: 0.1980 chunk 147 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 266 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 359 ASN E 189 GLN E 479 HIS B 197 HIS B 337 HIS B 359 ASN C 110 HIS C 132 ASN F 371 HIS F 422 GLN J 172 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.112089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080957 restraints weight = 43957.334| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.58 r_work: 0.3078 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 25655 Z= 0.134 Angle : 0.532 13.532 34774 Z= 0.272 Chirality : 0.044 0.208 4104 Planarity : 0.004 0.045 4414 Dihedral : 5.341 78.409 3522 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.18 % Allowed : 20.12 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.51 (0.15), residues: 3174 helix: 1.69 (0.15), residues: 1286 sheet: -0.42 (0.25), residues: 450 loop : -0.62 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 51 HIS 0.007 0.001 HIS C 110 PHE 0.022 0.001 PHE J 214 TYR 0.022 0.001 TYR J 94 ARG 0.010 0.000 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 1086) hydrogen bonds : angle 4.02372 ( 3039) SS BOND : bond 0.11255 ( 1) SS BOND : angle 8.51592 ( 2) covalent geometry : bond 0.00300 (25654) covalent geometry : angle 0.52761 (34772) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 255 time to evaluate : 3.035 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8786 (ttm110) cc_final: 0.8381 (mpt90) REVERT: D 33 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8448 (tp30) REVERT: E 247 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7962 (mp0) REVERT: G 70 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7788 (mt-10) REVERT: G 103 ARG cc_start: 0.7889 (tpp80) cc_final: 0.7570 (mtt-85) REVERT: G 120 LYS cc_start: 0.8460 (mttt) cc_final: 0.8217 (mmtp) REVERT: G 121 ASP cc_start: 0.8491 (t0) cc_final: 0.8240 (t70) REVERT: G 149 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7866 (t) REVERT: G 245 ASP cc_start: 0.8550 (t0) cc_final: 0.8087 (t0) REVERT: I 50 GLU cc_start: 0.8492 (tp30) cc_final: 0.8262 (tp30) REVERT: I 217 GLU cc_start: 0.9122 (tp30) cc_final: 0.8683 (tp30) REVERT: I 227 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8114 (mt-10) REVERT: I 316 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8332 (tm) REVERT: I 325 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8428 (mm-40) REVERT: B 53 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6441 (p0) REVERT: B 126 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8286 (tp30) REVERT: B 161 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8391 (mp) REVERT: B 166 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: B 355 ILE cc_start: 0.8127 (mt) cc_final: 0.7811 (mm) REVERT: B 384 HIS cc_start: 0.7680 (m-70) cc_final: 0.7392 (m-70) REVERT: B 418 GLU cc_start: 0.8576 (tt0) cc_final: 0.7749 (tp30) REVERT: B 428 ARG cc_start: 0.7377 (mtm110) cc_final: 0.6712 (mmt180) REVERT: C 48 ASP cc_start: 0.8281 (m-30) cc_final: 0.8067 (m-30) REVERT: C 63 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8156 (ptp90) REVERT: C 172 ARG cc_start: 0.8126 (mmt180) cc_final: 0.7925 (mpt180) REVERT: C 319 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: F 250 ARG cc_start: 0.7397 (ptp90) cc_final: 0.7119 (mtm-85) REVERT: F 364 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8438 (mtp85) REVERT: H 14 MET cc_start: 0.8256 (mmm) cc_final: 0.7663 (tmt) REVERT: H 95 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: H 245 ASP cc_start: 0.8622 (t0) cc_final: 0.8032 (t0) REVERT: H 284 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8229 (mp) REVERT: J 37 TRP cc_start: 0.7239 (t60) cc_final: 0.6874 (t60) REVERT: J 50 GLU cc_start: 0.7459 (tp30) cc_final: 0.6846 (tp30) REVERT: J 72 LYS cc_start: 0.7805 (mttp) cc_final: 0.7569 (ttmm) REVERT: J 98 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7436 (mmtm) REVERT: J 99 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7505 (p) REVERT: J 100 ASP cc_start: 0.8045 (m-30) cc_final: 0.7579 (m-30) REVERT: J 194 ARG cc_start: 0.7671 (tpt90) cc_final: 0.7404 (tpt90) REVERT: J 321 GLU cc_start: 0.8676 (tp30) cc_final: 0.8089 (tp30) outliers start: 116 outliers final: 51 residues processed: 352 average time/residue: 1.3589 time to fit residues: 556.1085 Evaluate side-chains 286 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 188 GLN Chi-restraints excluded: chain J residue 224 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 232 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 312 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 141 optimal weight: 0.0030 chunk 221 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 359 ASN B 197 HIS B 359 ASN C 110 HIS F 455 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.078485 restraints weight = 43993.367| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.62 r_work: 0.3068 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 25655 Z= 0.165 Angle : 0.559 13.581 34774 Z= 0.286 Chirality : 0.044 0.210 4104 Planarity : 0.004 0.048 4414 Dihedral : 5.280 77.605 3518 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.72 % Allowed : 19.79 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.64 (0.15), residues: 3174 helix: 1.76 (0.15), residues: 1286 sheet: -0.44 (0.24), residues: 466 loop : -0.47 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 51 HIS 0.007 0.001 HIS C 110 PHE 0.024 0.001 PHE J 214 TYR 0.017 0.001 TYR J 94 ARG 0.009 0.000 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 1086) hydrogen bonds : angle 4.02235 ( 3039) SS BOND : bond 0.11098 ( 1) SS BOND : angle 8.51945 ( 2) covalent geometry : bond 0.00383 (25654) covalent geometry : angle 0.55552 (34772) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 236 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 217 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8219 (ptm) REVERT: E 247 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8013 (mp0) REVERT: G 70 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7745 (mt-10) REVERT: G 103 ARG cc_start: 0.7888 (tpp80) cc_final: 0.7538 (mtt-85) REVERT: G 120 LYS cc_start: 0.8480 (mttt) cc_final: 0.8206 (mmtp) REVERT: G 121 ASP cc_start: 0.8589 (t0) cc_final: 0.8340 (t70) REVERT: G 244 GLN cc_start: 0.8697 (mt0) cc_final: 0.8469 (mp10) REVERT: G 245 ASP cc_start: 0.8550 (t0) cc_final: 0.8136 (t0) REVERT: I 316 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8318 (tm) REVERT: B 53 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6439 (p0) REVERT: B 126 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: B 161 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8367 (mp) REVERT: B 166 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7426 (tp30) REVERT: B 355 ILE cc_start: 0.8158 (mt) cc_final: 0.7866 (mm) REVERT: B 358 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: B 384 HIS cc_start: 0.7669 (m-70) cc_final: 0.7392 (m-70) REVERT: B 418 GLU cc_start: 0.8633 (tt0) cc_final: 0.7838 (tp30) REVERT: B 428 ARG cc_start: 0.7504 (mtm110) cc_final: 0.6689 (mmt90) REVERT: C 48 ASP cc_start: 0.8325 (m-30) cc_final: 0.8101 (m-30) REVERT: C 172 ARG cc_start: 0.8125 (mmt180) cc_final: 0.7865 (mpt180) REVERT: C 319 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: F 250 ARG cc_start: 0.7373 (ptp90) cc_final: 0.7087 (mtm-85) REVERT: F 364 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8429 (mtp180) REVERT: H 8 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: H 14 MET cc_start: 0.8292 (mmm) cc_final: 0.7752 (tmt) REVERT: H 95 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7942 (pt0) REVERT: H 245 ASP cc_start: 0.8643 (t0) cc_final: 0.8080 (t0) REVERT: H 284 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8274 (mp) REVERT: J 2 GLU cc_start: 0.7335 (tt0) cc_final: 0.7132 (tt0) REVERT: J 37 TRP cc_start: 0.7099 (t60) cc_final: 0.6771 (t60) REVERT: J 44 GLU cc_start: 0.8525 (tp30) cc_final: 0.7953 (tp30) REVERT: J 50 GLU cc_start: 0.7368 (tp30) cc_final: 0.6996 (tp30) REVERT: J 72 LYS cc_start: 0.7734 (mttp) cc_final: 0.7513 (ttpp) REVERT: J 98 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7507 (mmtp) REVERT: J 100 ASP cc_start: 0.8090 (m-30) cc_final: 0.7617 (m-30) REVERT: J 194 ARG cc_start: 0.7650 (tpt90) cc_final: 0.7355 (tpt90) REVERT: J 309 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5911 (tt) REVERT: J 319 TYR cc_start: 0.8512 (t80) cc_final: 0.8212 (t80) REVERT: J 321 GLU cc_start: 0.8721 (tp30) cc_final: 0.8406 (tp30) outliers start: 131 outliers final: 55 residues processed: 340 average time/residue: 1.3196 time to fit residues: 533.0698 Evaluate side-chains 279 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 210 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 224 ILE Chi-restraints excluded: chain J residue 309 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 126 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 194 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 301 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 300 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 189 GLN E 281 ASN I 323 ASN B 197 HIS C 110 HIS F 455 ASN J 172 ASN ** J 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.111456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.080073 restraints weight = 43907.833| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.60 r_work: 0.3089 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 25655 Z= 0.121 Angle : 0.521 12.418 34774 Z= 0.267 Chirality : 0.043 0.170 4104 Planarity : 0.004 0.047 4414 Dihedral : 5.010 76.749 3512 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.35 % Allowed : 21.02 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.82 (0.15), residues: 3174 helix: 1.85 (0.15), residues: 1294 sheet: -0.28 (0.24), residues: 454 loop : -0.34 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 111 HIS 0.006 0.001 HIS C 110 PHE 0.026 0.001 PHE H 75 TYR 0.020 0.001 TYR J 94 ARG 0.008 0.000 ARG J 324 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 1086) hydrogen bonds : angle 3.91064 ( 3039) SS BOND : bond 0.11257 ( 1) SS BOND : angle 8.41669 ( 2) covalent geometry : bond 0.00265 (25654) covalent geometry : angle 0.51726 (34772) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 241 time to evaluate : 4.192 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8793 (ttm110) cc_final: 0.8449 (mtt-85) REVERT: A 305 MET cc_start: 0.8735 (mmm) cc_final: 0.8361 (mmp) REVERT: E 247 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7997 (mp0) REVERT: E 283 GLU cc_start: 0.8796 (tp30) cc_final: 0.8302 (tm-30) REVERT: E 495 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8858 (pt0) REVERT: G 70 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7707 (mt-10) REVERT: G 103 ARG cc_start: 0.7834 (tpp80) cc_final: 0.7502 (mtt-85) REVERT: G 120 LYS cc_start: 0.8484 (mttt) cc_final: 0.8175 (mmtt) REVERT: G 121 ASP cc_start: 0.8654 (t0) cc_final: 0.8391 (t70) REVERT: G 244 GLN cc_start: 0.8690 (mt0) cc_final: 0.8418 (mp10) REVERT: G 245 ASP cc_start: 0.8482 (t0) cc_final: 0.8067 (t0) REVERT: I 316 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8371 (tm) REVERT: I 325 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8374 (mm-40) REVERT: B 53 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6511 (p0) REVERT: B 126 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: B 166 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7415 (tp30) REVERT: B 355 ILE cc_start: 0.8141 (mt) cc_final: 0.7841 (mm) REVERT: B 358 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: B 384 HIS cc_start: 0.7638 (m-70) cc_final: 0.7311 (m-70) REVERT: B 418 GLU cc_start: 0.8514 (tt0) cc_final: 0.7679 (tp30) REVERT: C 48 ASP cc_start: 0.8289 (m-30) cc_final: 0.8062 (m-30) REVERT: C 172 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7833 (mpt180) REVERT: C 228 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8323 (mmt90) REVERT: C 319 GLU cc_start: 0.8590 (pt0) cc_final: 0.8328 (pm20) REVERT: F 250 ARG cc_start: 0.7346 (ptp90) cc_final: 0.7062 (mtm-85) REVERT: F 310 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8006 (mm-30) REVERT: F 364 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8370 (mtp180) REVERT: H 8 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: H 14 MET cc_start: 0.8281 (mmm) cc_final: 0.7803 (tmt) REVERT: H 93 MET cc_start: 0.5706 (mmm) cc_final: 0.5444 (tpt) REVERT: H 95 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7954 (pt0) REVERT: H 245 ASP cc_start: 0.8613 (t0) cc_final: 0.8036 (t0) REVERT: J 37 TRP cc_start: 0.7195 (t60) cc_final: 0.6841 (t60) REVERT: J 50 GLU cc_start: 0.7418 (tp30) cc_final: 0.6983 (tp30) REVERT: J 72 LYS cc_start: 0.7686 (mttp) cc_final: 0.7483 (ttpp) REVERT: J 98 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7421 (mmtm) REVERT: J 100 ASP cc_start: 0.8072 (m-30) cc_final: 0.7610 (m-30) REVERT: J 194 ARG cc_start: 0.7594 (tpt90) cc_final: 0.7319 (tpt90) REVERT: J 319 TYR cc_start: 0.8515 (t80) cc_final: 0.8182 (t80) REVERT: J 321 GLU cc_start: 0.8832 (tp30) cc_final: 0.8190 (tp30) outliers start: 93 outliers final: 50 residues processed: 319 average time/residue: 1.5239 time to fit residues: 569.0442 Evaluate side-chains 278 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 218 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 495 GLU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 179 GLU Chi-restraints excluded: chain J residue 188 GLN Chi-restraints excluded: chain J residue 224 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 221 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 299 optimal weight: 7.9990 chunk 307 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 304 optimal weight: 6.9990 chunk 94 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN D 132 ASN B 197 HIS B 255 GLN F 455 ASN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN J 203 HIS J 323 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.110891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.079557 restraints weight = 43975.614| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.59 r_work: 0.3079 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 25655 Z= 0.134 Angle : 0.539 15.082 34774 Z= 0.273 Chirality : 0.043 0.188 4104 Planarity : 0.004 0.049 4414 Dihedral : 4.834 75.762 3505 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.79 % Allowed : 20.98 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.94 (0.16), residues: 3174 helix: 1.96 (0.15), residues: 1282 sheet: -0.23 (0.25), residues: 454 loop : -0.26 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.004 0.001 HIS D 97 PHE 0.025 0.001 PHE B 57 TYR 0.022 0.001 TYR J 94 ARG 0.007 0.000 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 1086) hydrogen bonds : angle 3.87775 ( 3039) SS BOND : bond 0.11232 ( 1) SS BOND : angle 8.35604 ( 2) covalent geometry : bond 0.00301 (25654) covalent geometry : angle 0.53511 (34772) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 233 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8800 (ttm110) cc_final: 0.8450 (mtt-85) REVERT: A 329 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8903 (m-30) REVERT: D 9 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7751 (t) REVERT: E 247 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8024 (mp0) REVERT: E 283 GLU cc_start: 0.8807 (tp30) cc_final: 0.8311 (tm-30) REVERT: G 70 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7716 (mt-10) REVERT: G 103 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7493 (mtt-85) REVERT: G 120 LYS cc_start: 0.8462 (mttt) cc_final: 0.8207 (mmtp) REVERT: G 121 ASP cc_start: 0.8649 (t0) cc_final: 0.8407 (t70) REVERT: G 244 GLN cc_start: 0.8705 (mt0) cc_final: 0.8426 (mp10) REVERT: G 245 ASP cc_start: 0.8498 (t0) cc_final: 0.8081 (t0) REVERT: I 307 GLU cc_start: 0.7959 (pt0) cc_final: 0.7468 (pp20) REVERT: I 316 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8374 (tm) REVERT: I 325 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8338 (mm-40) REVERT: B 53 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6701 (p0) REVERT: B 166 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7409 (tp30) REVERT: B 355 ILE cc_start: 0.8144 (mt) cc_final: 0.7845 (mm) REVERT: B 358 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7830 (tp30) REVERT: B 384 HIS cc_start: 0.7626 (m-70) cc_final: 0.7311 (m-70) REVERT: B 418 GLU cc_start: 0.8498 (tt0) cc_final: 0.7674 (tp30) REVERT: C 172 ARG cc_start: 0.8121 (mmt180) cc_final: 0.7868 (mpt180) REVERT: C 228 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8362 (mmt90) REVERT: C 319 GLU cc_start: 0.8612 (pt0) cc_final: 0.8346 (pm20) REVERT: F 250 ARG cc_start: 0.7300 (ptp90) cc_final: 0.7044 (mtm-85) REVERT: F 292 ARG cc_start: 0.7921 (mpp-170) cc_final: 0.7659 (mpp-170) REVERT: F 310 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8040 (mm-30) REVERT: F 364 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8387 (mtp180) REVERT: H 14 MET cc_start: 0.8403 (mmm) cc_final: 0.7879 (tmt) REVERT: H 93 MET cc_start: 0.5763 (mmm) cc_final: 0.5505 (tpt) REVERT: H 95 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8073 (pt0) REVERT: H 245 ASP cc_start: 0.8584 (t0) cc_final: 0.8038 (t0) REVERT: H 284 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8212 (mp) REVERT: J 37 TRP cc_start: 0.7213 (t60) cc_final: 0.6882 (t60) REVERT: J 44 GLU cc_start: 0.8457 (tp30) cc_final: 0.8148 (tp30) REVERT: J 50 GLU cc_start: 0.7375 (tp30) cc_final: 0.6971 (tp30) REVERT: J 72 LYS cc_start: 0.7721 (mttp) cc_final: 0.7484 (ttpp) REVERT: J 98 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7435 (mmtp) REVERT: J 100 ASP cc_start: 0.8069 (m-30) cc_final: 0.7604 (m-30) REVERT: J 216 MET cc_start: 0.7845 (mmt) cc_final: 0.7586 (mmt) REVERT: J 319 TYR cc_start: 0.8582 (t80) cc_final: 0.8189 (t80) REVERT: J 321 GLU cc_start: 0.8748 (tp30) cc_final: 0.8363 (tp30) REVERT: J 323 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8414 (m110) outliers start: 105 outliers final: 55 residues processed: 320 average time/residue: 1.4965 time to fit residues: 559.3909 Evaluate side-chains 293 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 227 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 297 SER Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 323 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 109 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 111 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN D 132 ASN B 197 HIS F 455 ASN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN J 323 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.110466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.079329 restraints weight = 43912.967| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.61 r_work: 0.3082 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 25655 Z= 0.134 Angle : 0.536 13.889 34774 Z= 0.273 Chirality : 0.043 0.193 4104 Planarity : 0.004 0.050 4414 Dihedral : 4.830 74.734 3505 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.50 % Allowed : 21.38 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.95 (0.16), residues: 3174 helix: 1.91 (0.15), residues: 1294 sheet: -0.20 (0.24), residues: 466 loop : -0.22 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.003 0.001 HIS B 197 PHE 0.023 0.001 PHE J 214 TYR 0.022 0.001 TYR J 94 ARG 0.007 0.000 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 1086) hydrogen bonds : angle 3.87229 ( 3039) SS BOND : bond 0.11235 ( 1) SS BOND : angle 8.33475 ( 2) covalent geometry : bond 0.00304 (25654) covalent geometry : angle 0.53180 (34772) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 235 time to evaluate : 4.289 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8810 (ttm110) cc_final: 0.8461 (mtt-85) REVERT: A 329 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8900 (m-30) REVERT: E 247 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8032 (mp0) REVERT: E 283 GLU cc_start: 0.8792 (tp30) cc_final: 0.8301 (tm-30) REVERT: G 70 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7709 (mt-10) REVERT: G 103 ARG cc_start: 0.7834 (tpp80) cc_final: 0.7494 (mtt-85) REVERT: G 120 LYS cc_start: 0.8458 (mttt) cc_final: 0.8214 (mmtp) REVERT: G 121 ASP cc_start: 0.8642 (t0) cc_final: 0.8420 (t70) REVERT: G 245 ASP cc_start: 0.8506 (t0) cc_final: 0.8099 (t0) REVERT: I 307 GLU cc_start: 0.7916 (pt0) cc_final: 0.7467 (pp20) REVERT: I 316 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8364 (tm) REVERT: I 325 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8368 (mm-40) REVERT: B 53 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6745 (p0) REVERT: B 126 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8408 (tp30) REVERT: B 166 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7418 (tp30) REVERT: B 355 ILE cc_start: 0.8159 (mt) cc_final: 0.7864 (mm) REVERT: B 358 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7800 (tp30) REVERT: B 384 HIS cc_start: 0.7598 (m-70) cc_final: 0.7279 (m-70) REVERT: B 418 GLU cc_start: 0.8504 (tt0) cc_final: 0.7670 (tp30) REVERT: B 455 ASP cc_start: 0.3821 (OUTLIER) cc_final: 0.3504 (p0) REVERT: C 63 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7848 (ptp90) REVERT: C 172 ARG cc_start: 0.8088 (mmt180) cc_final: 0.7859 (mpt180) REVERT: C 228 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8374 (mmt90) REVERT: C 319 GLU cc_start: 0.8613 (pt0) cc_final: 0.8343 (pm20) REVERT: F 250 ARG cc_start: 0.7312 (ptp90) cc_final: 0.7053 (mtm-85) REVERT: F 310 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8002 (mm-30) REVERT: F 364 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8382 (mtp180) REVERT: H 14 MET cc_start: 0.8459 (mmm) cc_final: 0.7876 (tmt) REVERT: H 93 MET cc_start: 0.5779 (mmm) cc_final: 0.5500 (tpt) REVERT: H 95 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8141 (pt0) REVERT: H 245 ASP cc_start: 0.8571 (t0) cc_final: 0.8038 (t0) REVERT: J 37 TRP cc_start: 0.7243 (t60) cc_final: 0.6864 (t60) REVERT: J 44 GLU cc_start: 0.8456 (tp30) cc_final: 0.8180 (tp30) REVERT: J 50 GLU cc_start: 0.7400 (tp30) cc_final: 0.6956 (tp30) REVERT: J 72 LYS cc_start: 0.7715 (mttp) cc_final: 0.7479 (ttpp) REVERT: J 98 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7440 (mmtm) REVERT: J 100 ASP cc_start: 0.8037 (m-30) cc_final: 0.7570 (m-30) REVERT: J 227 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8220 (mt-10) REVERT: J 319 TYR cc_start: 0.8542 (t80) cc_final: 0.8133 (t80) REVERT: J 321 GLU cc_start: 0.8843 (tp30) cc_final: 0.8249 (tp30) REVERT: J 323 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8487 (m110) outliers start: 97 outliers final: 55 residues processed: 314 average time/residue: 1.6284 time to fit residues: 605.3776 Evaluate side-chains 280 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 213 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 297 SER Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 323 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 210 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 294 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 296 optimal weight: 0.5980 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 359 ASN B 197 HIS F 265 GLN F 455 ASN F 470 HIS J 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.111055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.079953 restraints weight = 44000.885| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.57 r_work: 0.3116 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 25655 Z= 0.129 Angle : 0.546 13.605 34774 Z= 0.277 Chirality : 0.043 0.183 4104 Planarity : 0.004 0.049 4414 Dihedral : 4.814 73.540 3505 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.14 % Allowed : 22.06 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 3174 helix: 1.97 (0.15), residues: 1294 sheet: -0.13 (0.25), residues: 466 loop : -0.16 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.008 0.001 HIS F 470 PHE 0.026 0.001 PHE B 57 TYR 0.021 0.001 TYR J 94 ARG 0.007 0.000 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 1086) hydrogen bonds : angle 3.85159 ( 3039) SS BOND : bond 0.11266 ( 1) SS BOND : angle 8.32881 ( 2) covalent geometry : bond 0.00288 (25654) covalent geometry : angle 0.54220 (34772) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 221 time to evaluate : 3.234 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8762 (ttm110) cc_final: 0.8413 (mtt-85) REVERT: D 9 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7828 (t) REVERT: E 247 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8026 (mp0) REVERT: E 283 GLU cc_start: 0.8770 (tp30) cc_final: 0.8285 (tm-30) REVERT: E 293 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: E 294 GLU cc_start: 0.8023 (mp0) cc_final: 0.7742 (mp0) REVERT: G 70 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7742 (mt-10) REVERT: G 103 ARG cc_start: 0.7835 (tpp80) cc_final: 0.7493 (mtt-85) REVERT: G 120 LYS cc_start: 0.8473 (mttt) cc_final: 0.8254 (mmtp) REVERT: G 121 ASP cc_start: 0.8654 (t0) cc_final: 0.8404 (t70) REVERT: G 245 ASP cc_start: 0.8472 (t0) cc_final: 0.8066 (t0) REVERT: I 307 GLU cc_start: 0.7943 (pt0) cc_final: 0.7583 (pp20) REVERT: I 316 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8371 (tm) REVERT: I 325 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8336 (mm-40) REVERT: B 53 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6728 (p0) REVERT: B 126 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8459 (tp30) REVERT: B 166 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: B 355 ILE cc_start: 0.8194 (mt) cc_final: 0.7888 (mm) REVERT: B 358 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7772 (tp30) REVERT: B 384 HIS cc_start: 0.7672 (m-70) cc_final: 0.7362 (m-70) REVERT: B 418 GLU cc_start: 0.8482 (tt0) cc_final: 0.7683 (tp30) REVERT: C 63 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7852 (ptp90) REVERT: C 172 ARG cc_start: 0.8118 (mmt180) cc_final: 0.7875 (mpt180) REVERT: C 228 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8371 (mmt90) REVERT: C 319 GLU cc_start: 0.8574 (pt0) cc_final: 0.8310 (pm20) REVERT: F 250 ARG cc_start: 0.7335 (ptp90) cc_final: 0.7077 (mtm-85) REVERT: F 310 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7977 (mm-30) REVERT: F 364 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8342 (mtp180) REVERT: F 470 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7837 (p-80) REVERT: H 20 MET cc_start: 0.6977 (ttt) cc_final: 0.6346 (ppp) REVERT: H 95 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8158 (pt0) REVERT: H 198 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8791 (mt-10) REVERT: H 245 ASP cc_start: 0.8551 (t0) cc_final: 0.8024 (t0) REVERT: J 37 TRP cc_start: 0.7296 (t60) cc_final: 0.6930 (t60) REVERT: J 98 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7449 (mmtm) REVERT: J 99 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7544 (p) REVERT: J 100 ASP cc_start: 0.8072 (m-30) cc_final: 0.7627 (m-30) REVERT: J 216 MET cc_start: 0.7323 (mmt) cc_final: 0.7064 (mmt) REVERT: J 319 TYR cc_start: 0.8574 (t80) cc_final: 0.8264 (t80) REVERT: J 325 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.9066 (mt0) outliers start: 87 outliers final: 53 residues processed: 291 average time/residue: 1.3281 time to fit residues: 451.3910 Evaluate side-chains 282 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 215 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 297 SER Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 325 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 234 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 229 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 197 HIS F 455 ASN F 470 HIS J 172 ASN J 323 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.110618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.079533 restraints weight = 43905.713| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.55 r_work: 0.3097 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 25655 Z= 0.140 Angle : 0.554 13.303 34774 Z= 0.281 Chirality : 0.043 0.192 4104 Planarity : 0.004 0.048 4414 Dihedral : 4.832 72.621 3505 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.78 % Allowed : 22.39 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.16), residues: 3174 helix: 1.96 (0.15), residues: 1294 sheet: -0.12 (0.24), residues: 486 loop : -0.15 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.011 0.001 HIS F 470 PHE 0.036 0.001 PHE H 75 TYR 0.020 0.001 TYR J 94 ARG 0.008 0.000 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 1086) hydrogen bonds : angle 3.87214 ( 3039) SS BOND : bond 0.11219 ( 1) SS BOND : angle 8.32626 ( 2) covalent geometry : bond 0.00318 (25654) covalent geometry : angle 0.55034 (34772) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 213 time to evaluate : 2.939 Fit side-chains revert: symmetry clash REVERT: D 9 SER cc_start: 0.8129 (OUTLIER) cc_final: 0.7858 (t) REVERT: E 247 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7985 (mp0) REVERT: E 250 ARG cc_start: 0.7652 (ptt90) cc_final: 0.7295 (ptt90) REVERT: E 283 GLU cc_start: 0.8789 (tp30) cc_final: 0.8295 (tm-30) REVERT: G 70 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7738 (mt-10) REVERT: G 103 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7457 (mtt-85) REVERT: G 120 LYS cc_start: 0.8474 (mttt) cc_final: 0.8269 (mmtp) REVERT: G 121 ASP cc_start: 0.8657 (t0) cc_final: 0.8418 (t70) REVERT: G 245 ASP cc_start: 0.8484 (t0) cc_final: 0.8082 (t0) REVERT: I 307 GLU cc_start: 0.7973 (pt0) cc_final: 0.7634 (pp20) REVERT: I 316 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8364 (tm) REVERT: I 325 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8339 (mm-40) REVERT: B 53 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6712 (p0) REVERT: B 126 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8463 (tp30) REVERT: B 166 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7459 (tp30) REVERT: B 355 ILE cc_start: 0.8171 (mt) cc_final: 0.7871 (mm) REVERT: B 358 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: B 384 HIS cc_start: 0.7699 (m-70) cc_final: 0.7376 (m-70) REVERT: B 418 GLU cc_start: 0.8513 (tt0) cc_final: 0.7729 (tp30) REVERT: C 63 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7865 (ptp90) REVERT: C 128 GLN cc_start: 0.7566 (pm20) cc_final: 0.7178 (tp40) REVERT: C 228 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8401 (mmt90) REVERT: C 319 GLU cc_start: 0.8601 (pt0) cc_final: 0.8336 (pm20) REVERT: F 250 ARG cc_start: 0.7337 (ptp90) cc_final: 0.7079 (mtm-85) REVERT: F 310 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7975 (mm-30) REVERT: F 364 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8363 (mtp180) REVERT: F 470 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7780 (p-80) REVERT: H 20 MET cc_start: 0.7332 (ttt) cc_final: 0.6434 (ppp) REVERT: H 95 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8207 (pt0) REVERT: H 198 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8801 (mt-10) REVERT: H 245 ASP cc_start: 0.8553 (t0) cc_final: 0.8020 (t0) REVERT: J 37 TRP cc_start: 0.7311 (t60) cc_final: 0.6952 (t60) REVERT: J 98 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7440 (mmtm) REVERT: J 99 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7582 (p) REVERT: J 100 ASP cc_start: 0.8071 (m-30) cc_final: 0.7622 (m-30) REVERT: J 216 MET cc_start: 0.7487 (mmt) cc_final: 0.7269 (mmt) REVERT: J 325 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.9056 (mt0) outliers start: 77 outliers final: 52 residues processed: 280 average time/residue: 1.6063 time to fit residues: 527.7593 Evaluate side-chains 274 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 6.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 297 SER Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 325 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 197 HIS B 333 GLN F 455 ASN F 470 HIS J 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.106636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.075256 restraints weight = 44309.336| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.57 r_work: 0.3020 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 25655 Z= 0.276 Angle : 0.671 13.301 34774 Z= 0.341 Chirality : 0.048 0.222 4104 Planarity : 0.004 0.049 4414 Dihedral : 5.216 72.745 3505 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.99 % Allowed : 22.64 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.61 (0.15), residues: 3174 helix: 1.57 (0.15), residues: 1310 sheet: -0.20 (0.24), residues: 474 loop : -0.44 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 350 HIS 0.023 0.001 HIS F 470 PHE 0.032 0.002 PHE H 75 TYR 0.028 0.002 TYR J 94 ARG 0.008 0.001 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 1086) hydrogen bonds : angle 4.15279 ( 3039) SS BOND : bond 0.10812 ( 1) SS BOND : angle 8.56925 ( 2) covalent geometry : bond 0.00670 (25654) covalent geometry : angle 0.66815 (34772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22304.74 seconds wall clock time: 388 minutes 38.16 seconds (23318.16 seconds total)