Starting phenix.real_space_refine on Mon Jul 6 23:54:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oo7_17006/07_2026/8oo7_17006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oo7_17006/07_2026/8oo7_17006.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8oo7_17006/07_2026/8oo7_17006.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oo7_17006/07_2026/8oo7_17006.cif" model { file = "/net/cci-nas-00/data/ceres_data/8oo7_17006/07_2026/8oo7_17006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oo7_17006/07_2026/8oo7_17006.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oo7_17006/07_2026/8oo7_17006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oo7_17006/07_2026/8oo7_17006.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.266 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 243 5.49 5 Mg 2 5.21 5 S 160 5.16 5 C 25026 2.51 5 N 7396 2.21 5 O 8192 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41024 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3352 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3511 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3401 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3414 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 14, 'TRANS': 428} Chain breaks: 1 Chain: "F" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3394 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 14, 'TRANS': 424} Chain breaks: 1 Chain: "G" Number of atoms: 5736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5736 Classifications: {'peptide': 704} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 670} Chain breaks: 2 Chain: "H" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 283 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 4545 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 173} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 615} Chain breaks: 5 Unresolved non-hydrogen bonds: 697 Unresolved non-hydrogen angles: 851 Unresolved non-hydrogen dihedrals: 571 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLU:plan': 32, 'ARG:plan': 30, 'GLN:plan1': 12, 'TYR:plan': 4, 'ASP:plan': 11, 'ASN:plan1': 6, 'TRP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 429 Chain: "K" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2306 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "L" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2327 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 602 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "O" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "P" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "R" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.75, per 1000 atoms: 0.21 Number of scatterers: 41024 At special positions: 0 Unit cell: (141.384, 180.018, 191.526, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 160 16.00 P 243 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 8192 8.00 N 7396 7.00 C 25026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.6 seconds 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8712 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 43 sheets defined 50.6% alpha, 11.3% beta 61 base pairs and 202 stacking pairs defined. Time for finding SS restraints: 5.52 Creating SS restraints... Processing helix chain 'A' and resid 43 through 59 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 100 through 103 removed outlier: 4.067A pdb=" N TYR A 103 " --> pdb=" O SER A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.503A pdb=" N VAL A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.699A pdb=" N LEU A 264 " --> pdb=" O MET A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 321 removed outlier: 4.041A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 368 through 383 Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.690A pdb=" N CYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 411 " --> pdb=" O CYS A 407 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 427 through 438 removed outlier: 3.527A pdb=" N ILE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'B' and resid 43 through 60 removed outlier: 3.538A pdb=" N HIS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 241 through 250 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 257 through 266 removed outlier: 6.833A pdb=" N GLN B 263 " --> pdb=" O MET B 260 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU B 264 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 290 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.729A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 388 through 402 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.889A pdb=" N LEU B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 427 through 438 removed outlier: 3.978A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'C' and resid 43 through 59 Processing helix chain 'C' and resid 76 through 89 Processing helix chain 'C' and resid 100 through 103 removed outlier: 3.530A pdb=" N TYR C 103 " --> pdb=" O SER C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 103' Processing helix chain 'C' and resid 108 through 120 Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 273 through 290 Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 309 through 321 removed outlier: 3.823A pdb=" N LYS C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 388 through 402 Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.552A pdb=" N CYS C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 420 Processing helix chain 'C' and resid 427 through 438 removed outlier: 4.156A pdb=" N GLU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.518A pdb=" N GLY D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.855A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 125 Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.663A pdb=" N ARG D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 304 through 315 removed outlier: 4.883A pdb=" N ARG D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 362 through 377 Processing helix chain 'D' and resid 382 through 396 removed outlier: 3.585A pdb=" N GLU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 415 removed outlier: 3.626A pdb=" N ILE D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR D 406 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 434 through 444 Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 95 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 106 through 109 removed outlier: 3.593A pdb=" N PHE E 109 " --> pdb=" O SER E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 174 through 184 Processing helix chain 'E' and resid 208 through 214 removed outlier: 5.121A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 250 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 257 through 262 removed outlier: 3.521A pdb=" N SER E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 285 Processing helix chain 'E' and resid 299 through 303 Processing helix chain 'E' and resid 304 through 315 removed outlier: 3.957A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 362 through 377 Processing helix chain 'E' and resid 382 through 397 Processing helix chain 'E' and resid 397 through 415 removed outlier: 3.998A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 432 Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 Processing helix chain 'F' and resid 114 through 126 removed outlier: 3.603A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 184 Processing helix chain 'F' and resid 209 through 213 removed outlier: 4.190A pdb=" N ARG F 212 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 252 removed outlier: 4.287A pdb=" N ARG F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.638A pdb=" N ARG F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 304 through 316 removed outlier: 4.041A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU F 316 " --> pdb=" O ASN F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 362 through 377 Processing helix chain 'F' and resid 382 through 397 Processing helix chain 'F' and resid 397 through 415 removed outlier: 4.031A pdb=" N THR F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 432 Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 446 through 449 Processing helix chain 'G' and resid 973 through 989 Processing helix chain 'G' and resid 1002 through 1019 Processing helix chain 'G' and resid 1029 through 1031 No H-bonds generated for 'chain 'G' and resid 1029 through 1031' Processing helix chain 'G' and resid 1032 through 1044 Processing helix chain 'G' and resid 1055 through 1063 Processing helix chain 'G' and resid 1064 through 1066 No H-bonds generated for 'chain 'G' and resid 1064 through 1066' Processing helix chain 'G' and resid 1086 through 1092 removed outlier: 3.754A pdb=" N VAL G1090 " --> pdb=" O TYR G1086 " (cutoff:3.500A) Processing helix chain 'G' and resid 1092 through 1097 Processing helix chain 'G' and resid 1108 through 1112 Processing helix chain 'G' and resid 1117 through 1125 removed outlier: 3.693A pdb=" N GLY G1125 " --> pdb=" O LYS G1121 " (cutoff:3.500A) Processing helix chain 'G' and resid 1142 through 1154 removed outlier: 3.708A pdb=" N LEU G1149 " --> pdb=" O GLU G1145 " (cutoff:3.500A) Processing helix chain 'G' and resid 1187 through 1194 removed outlier: 3.953A pdb=" N MET G1192 " --> pdb=" O LYS G1188 " (cutoff:3.500A) Processing helix chain 'G' and resid 1202 through 1207 Processing helix chain 'G' and resid 1223 through 1235 Processing helix chain 'G' and resid 1236 through 1239 Processing helix chain 'G' and resid 1257 through 1268 removed outlier: 3.654A pdb=" N MET G1262 " --> pdb=" O MET G1258 " (cutoff:3.500A) Processing helix chain 'G' and resid 1270 through 1275 removed outlier: 3.935A pdb=" N PHE G1274 " --> pdb=" O HIS G1270 " (cutoff:3.500A) Processing helix chain 'G' and resid 1316 through 1321 Processing helix chain 'G' and resid 1333 through 1345 removed outlier: 4.523A pdb=" N GLY G1337 " --> pdb=" O ASN G1333 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) Processing helix chain 'G' and resid 1351 through 1357 removed outlier: 3.636A pdb=" N SER G1357 " --> pdb=" O GLU G1353 " (cutoff:3.500A) Processing helix chain 'G' and resid 1365 through 1370 removed outlier: 3.769A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) Processing helix chain 'G' and resid 1374 through 1382 Processing helix chain 'G' and resid 1385 through 1394 Processing helix chain 'G' and resid 1398 through 1407 removed outlier: 3.745A pdb=" N ILE G1405 " --> pdb=" O GLY G1401 " (cutoff:3.500A) Processing helix chain 'G' and resid 1417 through 1421 Processing helix chain 'G' and resid 1423 through 1428 Processing helix chain 'G' and resid 1429 through 1435 removed outlier: 4.040A pdb=" N VAL G1433 " --> pdb=" O ASN G1429 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU G1435 " --> pdb=" O LYS G1431 " (cutoff:3.500A) Processing helix chain 'G' and resid 1440 through 1446 Processing helix chain 'G' and resid 1447 through 1456 Processing helix chain 'G' and resid 1480 through 1492 removed outlier: 3.577A pdb=" N VAL G1484 " --> pdb=" O SER G1480 " (cutoff:3.500A) Processing helix chain 'G' and resid 1493 through 1502 Processing helix chain 'G' and resid 1504 through 1514 Processing helix chain 'G' and resid 1544 through 1551 Processing helix chain 'G' and resid 1552 through 1569 Processing helix chain 'G' and resid 1578 through 1592 removed outlier: 3.588A pdb=" N ILE G1582 " --> pdb=" O MET G1578 " (cutoff:3.500A) Processing helix chain 'G' and resid 1604 through 1618 Processing helix chain 'G' and resid 1651 through 1661 removed outlier: 3.675A pdb=" N ASP G1655 " --> pdb=" O ASN G1651 " (cutoff:3.500A) Processing helix chain 'G' and resid 1681 through 1700 removed outlier: 3.920A pdb=" N ARG G1685 " --> pdb=" O THR G1681 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU G1695 " --> pdb=" O LEU G1691 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 475 removed outlier: 4.305A pdb=" N VAL H 473 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 21 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 190 through 200 Processing helix chain 'I' and resid 203 through 211 removed outlier: 3.787A pdb=" N GLN I 207 " --> pdb=" O GLY I 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.759A pdb=" N ARG J 46 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 225 through 228 Processing helix chain 'J' and resid 234 through 250 Processing helix chain 'J' and resid 259 through 271 removed outlier: 3.597A pdb=" N HIS J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 282 Processing helix chain 'J' and resid 289 through 294 Processing helix chain 'J' and resid 312 through 360 Processing helix chain 'J' and resid 363 through 370 removed outlier: 4.729A pdb=" N ARG J 367 " --> pdb=" O LYS J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 371 through 373 No H-bonds generated for 'chain 'J' and resid 371 through 373' Processing helix chain 'J' and resid 376 through 394 removed outlier: 4.411A pdb=" N ARG J 382 " --> pdb=" O ALA J 378 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL J 383 " --> pdb=" O ALA J 379 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 498 removed outlier: 7.302A pdb=" N GLU J 471 " --> pdb=" O LYS J 467 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY J 472 " --> pdb=" O ASN J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 514 removed outlier: 4.272A pdb=" N SER J 506 " --> pdb=" O LYS J 502 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET J 510 " --> pdb=" O SER J 506 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS J 511 " --> pdb=" O GLN J 507 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN J 512 " --> pdb=" O ILE J 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 575 through 589 Processing helix chain 'J' and resid 593 through 597 Processing helix chain 'J' and resid 599 through 606 removed outlier: 7.084A pdb=" N TRP J 604 " --> pdb=" O GLN J 601 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N SER J 605 " --> pdb=" O ARG J 602 " (cutoff:3.500A) Processing helix chain 'J' and resid 607 through 615 removed outlier: 3.606A pdb=" N ALA J 611 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 639 Processing helix chain 'J' and resid 640 through 643 Processing helix chain 'J' and resid 645 through 650 Processing helix chain 'J' and resid 656 through 668 Processing helix chain 'J' and resid 679 through 684 Processing helix chain 'J' and resid 690 through 694 Processing helix chain 'J' and resid 697 through 710 removed outlier: 3.620A pdb=" N ALA J 708 " --> pdb=" O GLN J 704 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU J 709 " --> pdb=" O GLY J 705 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 736 removed outlier: 3.766A pdb=" N ALA J 732 " --> pdb=" O ALA J 728 " (cutoff:3.500A) Processing helix chain 'J' and resid 738 through 743 Processing helix chain 'J' and resid 748 through 755 removed outlier: 3.680A pdb=" N GLU J 753 " --> pdb=" O GLU J 749 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 113 removed outlier: 3.637A pdb=" N MET M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 116 No H-bonds generated for 'chain 'M' and resid 114 through 116' Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.604A pdb=" N ILE N 29 " --> pdb=" O ILE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.511A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 95 Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 46 through 73 Processing helix chain 'O' and resid 79 through 89 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 34 through 46 Processing helix chain 'P' and resid 52 through 81 Processing helix chain 'P' and resid 87 through 99 Processing helix chain 'P' and resid 100 through 122 removed outlier: 3.501A pdb=" N ALA P 104 " --> pdb=" O PRO P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 55 Processing helix chain 'Q' and resid 63 through 79 removed outlier: 3.946A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE Q 78 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.515A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 29 Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.629A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 98 removed outlier: 6.271A pdb=" N VAL A 67 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER A 332 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 69 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 144 removed outlier: 6.124A pdb=" N GLY A 161 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET A 139 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 159 " --> pdb=" O MET A 139 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A 157 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLU A 143 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 155 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 167 " --> pdb=" O SER A 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 167 through 173 current: chain 'A' and resid 201 through 207 removed outlier: 6.080A pdb=" N VAL A 222 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG A 206 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 339 removed outlier: 5.655A pdb=" N LEU A 345 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 37 Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 98 removed outlier: 6.316A pdb=" N CYS B 95 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASP B 303 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 97 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY B 66 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B 362 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 68 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR B 364 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA B 70 " --> pdb=" O THR B 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 141 removed outlier: 5.531A pdb=" N VAL B 136 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS B 163 " --> pdb=" O VAL B 136 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 167 through 173 current: chain 'B' and resid 201 through 207 removed outlier: 6.395A pdb=" N VAL B 222 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARG B 206 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 336 through 339 removed outlier: 5.838A pdb=" N LEU B 345 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB1, first strand: chain 'C' and resid 94 through 98 removed outlier: 6.922A pdb=" N GLY C 66 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE C 362 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 68 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR C 364 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA C 70 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 121 through 143 removed outlier: 5.597A pdb=" N VAL C 136 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS C 163 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 138 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 167 " --> pdb=" O SER C 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 173 current: chain 'C' and resid 201 through 207 removed outlier: 6.535A pdb=" N VAL C 222 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ARG C 206 " --> pdb=" O VAL C 222 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 221 through 222 current: chain 'D' and resid 156 through 163 removed outlier: 3.695A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 168 through 173 current: chain 'D' and resid 201 through 206 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 201 through 206 current: chain 'H' and resid 456 through 461 Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 339 removed outlier: 6.042A pdb=" N LEU C 345 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 104 Processing sheet with id=AB6, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AB7, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.533A pdb=" N THR E 101 " --> pdb=" O PHE E 296 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASP E 298 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU E 103 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA E 72 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE E 356 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU E 74 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 127 through 147 removed outlier: 6.576A pdb=" N THR E 161 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE E 145 " --> pdb=" O LYS E 159 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS E 159 " --> pdb=" O ILE E 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 168 through 172 current: chain 'E' and resid 201 through 206 Processing sheet with id=AC1, first strand: chain 'E' and resid 331 through 333 Processing sheet with id=AC2, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.635A pdb=" N THR F 101 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP F 298 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU F 103 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA F 72 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE F 356 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU F 74 " --> pdb=" O ILE F 356 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 236 through 242 Processing sheet with id=AC5, first strand: chain 'F' and resid 137 through 148 removed outlier: 6.681A pdb=" N THR F 161 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE F 145 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS F 159 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE F 147 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN F 157 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY F 158 " --> pdb=" O MET F 173 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 168 through 173 current: chain 'F' and resid 201 through 207 removed outlier: 6.684A pdb=" N LEU F 224 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG F 206 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 331 through 333 Processing sheet with id=AC7, first strand: chain 'G' and resid 1049 through 1051 removed outlier: 6.222A pdb=" N PHE G1024 " --> pdb=" O MET G1082 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR G1084 " --> pdb=" O PHE G1024 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL G1026 " --> pdb=" O THR G1084 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET G1104 " --> pdb=" O LEU G1132 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU G1134 " --> pdb=" O MET G1104 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU G1106 " --> pdb=" O LEU G1134 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY G 993 " --> pdb=" O LEU G1133 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE G 994 " --> pdb=" O LEU G1199 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 1100 through 1101 Processing sheet with id=AC9, first strand: chain 'G' and resid 1214 through 1217 removed outlier: 6.235A pdb=" N ILE G1214 " --> pdb=" O VAL G1673 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ARG G1675 " --> pdb=" O ILE G1214 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE G1216 " --> pdb=" O ARG G1675 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL G1643 " --> pdb=" O TYR G1674 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU G1573 " --> pdb=" O ILE G1644 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL G1572 " --> pdb=" O PHE G1624 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU G1626 " --> pdb=" O VAL G1572 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU G1574 " --> pdb=" O LEU G1626 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N CYS G1597 " --> pdb=" O LEU G1625 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N SER G1627 " --> pdb=" O CYS G1597 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU G1599 " --> pdb=" O SER G1627 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 1220 through 1221 removed outlier: 6.415A pdb=" N CYS G1220 " --> pdb=" O ARG G1679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 1283 through 1284 removed outlier: 6.073A pdb=" N PHE G1283 " --> pdb=" O SER G1470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'G' and resid 1286 through 1287 Processing sheet with id=AD4, first strand: chain 'G' and resid 1312 through 1314 removed outlier: 6.045A pdb=" N TYR G1313 " --> pdb=" O VAL G1477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'I' and resid 179 through 180 removed outlier: 3.808A pdb=" N TYR I 179 " --> pdb=" O TYR I 188 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 27 through 29 Processing sheet with id=AD7, first strand: chain 'J' and resid 80 through 82 removed outlier: 4.435A pdb=" N ASN J 63 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 97 through 100 Processing sheet with id=AD9, first strand: chain 'J' and resid 203 through 208 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 222 through 223 current: chain 'J' and resid 718 through 720 Processing sheet with id=AE1, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.700A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AE3, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.172A pdb=" N ARG O 42 " --> pdb=" O ILE P 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AE5, first strand: chain 'O' and resid 101 through 102 removed outlier: 6.523A pdb=" N THR O 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.548A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'Q' and resid 118 through 119 1702 hydrogen bonds defined for protein. 4905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 151 hydrogen bonds 302 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 202 stacking parallelities Total time for adding SS restraints: 12.59 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13101 1.34 - 1.46: 6958 1.46 - 1.58: 21362 1.58 - 1.69: 475 1.69 - 1.81: 279 Bond restraints: 42175 Sorted by residual: bond pdb=" F3 ALF G1901 " pdb="AL ALF G1901 " ideal model delta sigma weight residual 1.685 1.802 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" F1 ALF G1901 " pdb="AL ALF G1901 " ideal model delta sigma weight residual 1.684 1.800 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" F4 ALF G1901 " pdb="AL ALF G1901 " ideal model delta sigma weight residual 1.686 1.786 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F2 ALF G1901 " pdb="AL ALF G1901 " ideal model delta sigma weight residual 1.685 1.772 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C3' DC L 60 " pdb=" C2' DC L 60 " ideal model delta sigma weight residual 1.516 1.530 -0.014 8.00e-03 1.56e+04 3.12e+00 ... (remaining 42170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.09: 58000 14.09 - 28.18: 4 28.18 - 42.27: 0 42.27 - 56.36: 0 56.36 - 70.45: 2 Bond angle restraints: 58006 Sorted by residual: angle pdb=" F1 ALF G1901 " pdb="AL ALF G1901 " pdb=" F2 ALF G1901 " ideal model delta sigma weight residual 108.68 179.13 -70.45 3.00e+00 1.11e-01 5.52e+02 angle pdb=" F3 ALF G1901 " pdb="AL ALF G1901 " pdb=" F4 ALF G1901 " ideal model delta sigma weight residual 109.63 179.90 -70.27 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F2 ALF G1901 " pdb="AL ALF G1901 " pdb=" F4 ALF G1901 " ideal model delta sigma weight residual 110.21 89.69 20.52 3.00e+00 1.11e-01 4.68e+01 angle pdb=" F1 ALF G1901 " pdb="AL ALF G1901 " pdb=" F4 ALF G1901 " ideal model delta sigma weight residual 109.02 89.51 19.51 3.00e+00 1.11e-01 4.23e+01 angle pdb=" F2 ALF G1901 " pdb="AL ALF G1901 " pdb=" F3 ALF G1901 " ideal model delta sigma weight residual 109.59 90.27 19.32 3.00e+00 1.11e-01 4.15e+01 ... (remaining 58001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.24: 23591 33.24 - 66.47: 1390 66.47 - 99.71: 67 99.71 - 132.94: 4 132.94 - 166.18: 9 Dihedral angle restraints: 25061 sinusoidal: 11556 harmonic: 13505 Sorted by residual: dihedral pdb=" O1B ADP G1902 " pdb=" O3A ADP G1902 " pdb=" PB ADP G1902 " pdb=" PA ADP G1902 " ideal model delta sinusoidal sigma weight residual 300.00 133.82 166.18 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 102.47 -162.48 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 141.22 158.79 1 2.00e+01 2.50e-03 4.64e+01 ... (remaining 25058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 4241 0.044 - 0.087: 1757 0.087 - 0.131: 557 0.131 - 0.174: 46 0.174 - 0.218: 6 Chirality restraints: 6607 Sorted by residual: chirality pdb=" CB ILE N 29 " pdb=" CA ILE N 29 " pdb=" CG1 ILE N 29 " pdb=" CG2 ILE N 29 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA THR D 81 " pdb=" N THR D 81 " pdb=" C THR D 81 " pdb=" CB THR D 81 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA GLU J 635 " pdb=" N GLU J 635 " pdb=" C GLU J 635 " pdb=" CB GLU J 635 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 6604 not shown) Planarity restraints: 6684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 313 " -0.398 9.50e-02 1.11e+02 1.79e-01 2.49e+01 pdb=" NE ARG E 313 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG E 313 " -0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG E 313 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG E 313 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 252 " 0.362 9.50e-02 1.11e+02 1.63e-01 2.01e+01 pdb=" NE ARG D 252 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D 252 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG D 252 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG D 252 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 92 " -0.346 9.50e-02 1.11e+02 1.56e-01 1.86e+01 pdb=" NE ARG N 92 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG N 92 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG N 92 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG N 92 " -0.001 2.00e-02 2.50e+03 ... (remaining 6681 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 58 2.40 - 3.03: 23407 3.03 - 3.65: 63229 3.65 - 4.28: 101326 4.28 - 4.90: 161672 Nonbonded interactions: 349692 Sorted by model distance: nonbonded pdb="MG MG J 801 " pdb=" O1G ATP J 802 " model vdw 1.779 2.170 nonbonded pdb=" F3 ALF G1901 " pdb="MG MG G1903 " model vdw 1.898 2.120 nonbonded pdb=" O2B ADP G1902 " pdb="MG MG G1903 " model vdw 2.018 2.170 nonbonded pdb="MG MG J 801 " pdb=" O1B ATP J 802 " model vdw 2.026 2.170 nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 801 " model vdw 2.188 2.170 ... (remaining 349687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 144 or resid 156 through 501)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 144 or resid 156 through 501)) } ncs_group { reference = (chain 'D' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'F' and resid 20 through 501) } ncs_group { reference = (chain 'N' and resid 23 through 95) selection = (chain 'R' and resid 23 through 95) } 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=0.00 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: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 45.760 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 0.424 42176 Z= 0.303 Angle : 0.946 70.454 58006 Z= 0.516 Chirality : 0.050 0.218 6607 Planarity : 0.011 0.179 6684 Dihedral : 18.200 166.175 16349 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.11), residues: 4639 helix: -1.35 (0.09), residues: 2196 sheet: 0.45 (0.20), residues: 595 loop : -0.09 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.004 ARG E 313 TYR 0.031 0.005 TYR A 210 PHE 0.024 0.002 PHE C 117 TRP 0.041 0.003 TRP G1650 HIS 0.008 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.22 (42175) covalent geometry : angle 0.94593 / 0.52 (58006) hydrogen bonds : bond 0.20229 / 13.80 ( 1853) hydrogen bonds : angle 7.78750 / 5.57 ( 5207) Misc. bond : bond 0.42415 / 22.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 897 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7914 (tt0) cc_final: 0.7599 (tp30) REVERT: A 286 LYS cc_start: 0.7877 (mtpp) cc_final: 0.7672 (mtmm) REVERT: A 373 ARG cc_start: 0.8234 (ttm110) cc_final: 0.7810 (ttp80) REVERT: B 269 MET cc_start: 0.7666 (mtm) cc_final: 0.7407 (mtm) REVERT: B 419 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7845 (ttm170) REVERT: B 442 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.6975 (mmm160) REVERT: C 106 GLU cc_start: 0.8052 (tt0) cc_final: 0.7671 (mt-10) REVERT: C 303 ASP cc_start: 0.7350 (t0) cc_final: 0.6917 (t0) REVERT: C 368 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7744 (mm-30) REVERT: D 167 MET cc_start: 0.8729 (mtp) cc_final: 0.8438 (ttm) REVERT: D 232 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7792 (mm-40) REVERT: D 235 LYS cc_start: 0.8768 (tttt) cc_final: 0.8550 (ttpp) REVERT: E 263 ASP cc_start: 0.7096 (t0) cc_final: 0.6815 (t0) REVERT: E 273 ASP cc_start: 0.8003 (t0) cc_final: 0.7786 (t0) REVERT: E 302 MET cc_start: 0.8909 (mmm) cc_final: 0.8689 (mmp) REVERT: F 183 LYS cc_start: 0.8433 (mmmm) cc_final: 0.8196 (tptp) REVERT: F 299 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7530 (mm-30) REVERT: G 1235 ASN cc_start: 0.6953 (t0) cc_final: 0.6728 (t0) REVERT: G 1240 MET cc_start: 0.5627 (mmm) cc_final: 0.5227 (mpt) REVERT: G 1406 VAL cc_start: 0.7860 (t) cc_final: 0.7484 (m) REVERT: G 1479 ASP cc_start: 0.7239 (p0) cc_final: 0.6657 (p0) REVERT: G 1534 LYS cc_start: 0.8259 (tttt) cc_final: 0.8042 (mtpp) REVERT: G 1585 MET cc_start: 0.7651 (tpt) cc_final: 0.7143 (tpp) REVERT: J 677 ASP cc_start: 0.7857 (t0) cc_final: 0.7356 (t0) REVERT: N 91 LYS cc_start: 0.8224 (mttt) cc_final: 0.7378 (mptt) REVERT: O 74 LYS cc_start: 0.8135 (mttt) cc_final: 0.7931 (mtpm) REVERT: P 32 GLU cc_start: 0.5656 (mt-10) cc_final: 0.5346 (pt0) REVERT: P 68 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7257 (tp30) REVERT: P 75 SER cc_start: 0.8547 (t) cc_final: 0.8335 (m) REVERT: Q 79 LYS cc_start: 0.8232 (tptm) cc_final: 0.7872 (tmmt) REVERT: R 82 THR cc_start: 0.8094 (p) cc_final: 0.7670 (t) REVERT: R 95 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7372 (mtp-110) outliers start: 0 outliers final: 3 residues processed: 897 average time/residue: 0.9788 time to fit residues: 1021.8179 Evaluate side-chains 504 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 501 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain G residue 1508 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 470 optimal weight: 2.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 HIS B 255 GLN B 285 GLN B 421 ASN B 429 GLN C 19 HIS C 146 ASN C 237 GLN D 328 ASN E 24 HIS E 65 GLN F 96 GLN F 357 ASN F 394 GLN G1035 ASN G1151 HIS G1207 GLN G1269 ASN G1345 HIS I 199 ASN J 628 HIS M 125 GLN N 93 GLN P 60 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS P 81 ASN Q 68 GLN Q 125 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.109005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092680 restraints weight = 66693.224| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.70 r_work: 0.3237 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 42176 Z= 0.207 Angle : 0.778 31.796 58006 Z= 0.397 Chirality : 0.048 0.244 6607 Planarity : 0.005 0.073 6684 Dihedral : 21.559 175.743 7658 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.57 % Allowed : 10.14 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.12), residues: 4639 helix: 0.05 (0.10), residues: 2248 sheet: 0.30 (0.20), residues: 616 loop : 0.22 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 313 TYR 0.021 0.002 TYR D 310 PHE 0.025 0.002 PHE D 223 TRP 0.023 0.002 TRP G1650 HIS 0.010 0.002 HIS G1345 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (42175) covalent geometry : angle 0.77793 / 0.40 (58006) hydrogen bonds : bond 0.05976 / 4.07 ( 1853) hydrogen bonds : angle 5.09830 / 3.64 ( 5207) Misc. bond : bond 0.02193 / 1.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 514 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8695 (mttp) REVERT: A 228 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: A 286 LYS cc_start: 0.8069 (mtpp) cc_final: 0.7833 (mtmm) REVERT: A 373 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7902 (ttp80) REVERT: B 34 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6977 (mm-30) REVERT: B 419 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7939 (ttm170) REVERT: B 442 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7175 (mmm160) REVERT: C 106 GLU cc_start: 0.8146 (tt0) cc_final: 0.7779 (mt-10) REVERT: C 368 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7487 (mm-30) REVERT: D 184 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7776 (tp30) REVERT: D 187 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8226 (mmm) REVERT: D 228 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: D 232 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7877 (mm-40) REVERT: D 284 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: E 263 ASP cc_start: 0.7152 (t0) cc_final: 0.6924 (t0) REVERT: E 273 ASP cc_start: 0.8126 (t0) cc_final: 0.7923 (t0) REVERT: E 302 MET cc_start: 0.8931 (mmm) cc_final: 0.8720 (mmp) REVERT: E 312 ASN cc_start: 0.8692 (m-40) cc_final: 0.8406 (m110) REVERT: F 136 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: F 325 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8583 (ptp) REVERT: G 1235 ASN cc_start: 0.7211 (t0) cc_final: 0.6984 (t0) REVERT: G 1240 MET cc_start: 0.6105 (mmm) cc_final: 0.5622 (mpt) REVERT: G 1328 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8131 (mmmm) REVERT: G 1392 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: G 1479 ASP cc_start: 0.7072 (p0) cc_final: 0.6820 (p0) REVERT: H 455 MET cc_start: 0.8230 (mmm) cc_final: 0.7669 (mpp) REVERT: I 167 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8108 (mttm) REVERT: J 242 MET cc_start: 0.8620 (tpp) cc_final: 0.8362 (tpp) REVERT: J 635 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7138 (pm20) REVERT: J 677 ASP cc_start: 0.8063 (t0) cc_final: 0.7702 (t0) REVERT: M 120 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6835 (mmt) REVERT: N 31 LYS cc_start: 0.7253 (mttt) cc_final: 0.7023 (mtpt) REVERT: N 91 LYS cc_start: 0.8191 (mttt) cc_final: 0.7671 (mmtt) REVERT: P 31 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6745 (tmtm) REVERT: P 76 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7731 (ttm110) REVERT: R 59 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7362 (ttmt) REVERT: R 85 ASP cc_start: 0.6917 (m-30) cc_final: 0.6654 (t0) REVERT: R 95 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7411 (mtp-110) outliers start: 97 outliers final: 28 residues processed: 576 average time/residue: 0.8945 time to fit residues: 607.0429 Evaluate side-chains 491 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 447 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 968 LEU Chi-restraints excluded: chain G residue 1328 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1480 SER Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 454 LYS Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 447 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 381 optimal weight: 10.0000 chunk 257 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 438 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 421 ASN B 429 GLN C 146 ASN C 230 HIS D 328 ASN E 419 GLN F 96 GLN F 357 ASN G 989 GLN G1097 GLN G1207 GLN I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN N 93 GLN P 60 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS Q 68 GLN Q 108 ASN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.109281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.093010 restraints weight = 66483.737| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.63 r_work: 0.3250 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42176 Z= 0.159 Angle : 0.685 31.689 58006 Z= 0.345 Chirality : 0.045 0.203 6607 Planarity : 0.005 0.059 6684 Dihedral : 21.636 177.416 7651 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.39 % Allowed : 12.42 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.12), residues: 4639 helix: 0.57 (0.11), residues: 2249 sheet: 0.15 (0.20), residues: 634 loop : 0.30 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 442 TYR 0.066 0.002 TYR N 88 PHE 0.016 0.002 PHE C 117 TRP 0.015 0.002 TRP G1036 HIS 0.013 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (42175) covalent geometry : angle 0.68520 / 0.34 (58006) hydrogen bonds : bond 0.04765 / 3.24 ( 1853) hydrogen bonds : angle 4.61257 / 3.29 ( 5207) Misc. bond : bond 0.00460 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 494 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: A 278 MET cc_start: 0.8526 (tpp) cc_final: 0.8200 (mmm) REVERT: A 286 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7949 (mtmm) REVERT: A 373 ARG cc_start: 0.8317 (ttm110) cc_final: 0.7869 (ttp80) REVERT: B 34 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: B 429 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: B 442 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7172 (mmm160) REVERT: C 106 GLU cc_start: 0.8083 (tt0) cc_final: 0.7758 (mt-10) REVERT: C 307 MET cc_start: 0.8675 (mmt) cc_final: 0.8022 (mmt) REVERT: D 61 GLU cc_start: 0.8074 (tp30) cc_final: 0.7848 (tm-30) REVERT: D 232 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7835 (mm110) REVERT: D 284 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: E 263 ASP cc_start: 0.7114 (t0) cc_final: 0.6785 (t0) REVERT: E 273 ASP cc_start: 0.8052 (t0) cc_final: 0.7823 (m-30) REVERT: E 302 MET cc_start: 0.8899 (mmm) cc_final: 0.8678 (mmp) REVERT: E 312 ASN cc_start: 0.8681 (m-40) cc_final: 0.8410 (m110) REVERT: F 136 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: F 183 LYS cc_start: 0.8606 (tttp) cc_final: 0.8403 (tttt) REVERT: F 313 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7330 (tpp-160) REVERT: F 325 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8592 (ptp) REVERT: G 1235 ASN cc_start: 0.7281 (t0) cc_final: 0.7009 (t0) REVERT: G 1240 MET cc_start: 0.6092 (mmm) cc_final: 0.5655 (mpt) REVERT: G 1392 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: G 1429 ASN cc_start: 0.7888 (t0) cc_final: 0.7666 (t0) REVERT: I 167 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8107 (mttm) REVERT: J 174 GLU cc_start: 0.7836 (tt0) cc_final: 0.7582 (pt0) REVERT: J 242 MET cc_start: 0.8577 (tpp) cc_final: 0.8361 (tpp) REVERT: J 635 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: J 677 ASP cc_start: 0.8084 (t0) cc_final: 0.7758 (t0) REVERT: N 84 MET cc_start: 0.7855 (tpp) cc_final: 0.7541 (tpt) REVERT: N 91 LYS cc_start: 0.8110 (mttt) cc_final: 0.7582 (mptt) REVERT: P 31 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6761 (tttm) REVERT: Q 118 THR cc_start: 0.6800 (OUTLIER) cc_final: 0.6545 (t) REVERT: R 59 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7255 (ttmt) REVERT: R 78 ARG cc_start: 0.6887 (mtm110) cc_final: 0.6527 (mtm-85) REVERT: R 92 ARG cc_start: 0.7499 (ttt-90) cc_final: 0.7238 (ttt-90) REVERT: R 95 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7332 (mtp-110) outliers start: 90 outliers final: 25 residues processed: 549 average time/residue: 0.8777 time to fit residues: 567.0661 Evaluate side-chains 474 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 436 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 313 ARG Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 968 LEU Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 59 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 252 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 323 optimal weight: 6.9990 chunk 339 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 chunk 360 optimal weight: 1.9990 chunk 410 optimal weight: 30.0000 chunk 359 optimal weight: 3.9990 chunk 337 optimal weight: 8.9990 chunk 460 optimal weight: 6.9990 chunk 458 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 421 ASN B 429 GLN C 146 ASN C 182 GLN D 328 ASN E 328 ASN E 394 GLN F 96 GLN F 357 ASN G 989 GLN G1097 GLN I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 GLN N 64 ASN N 93 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.110142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093713 restraints weight = 66056.227| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.52 r_work: 0.3274 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42176 Z= 0.133 Angle : 0.652 30.302 58006 Z= 0.325 Chirality : 0.043 0.196 6607 Planarity : 0.004 0.072 6684 Dihedral : 21.434 169.344 7651 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.50 % Allowed : 13.86 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 4639 helix: 0.87 (0.11), residues: 2247 sheet: 0.21 (0.20), residues: 630 loop : 0.33 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 35 TYR 0.029 0.002 TYR G1591 PHE 0.026 0.001 PHE D 223 TRP 0.018 0.001 TRP G1036 HIS 0.008 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (42175) covalent geometry : angle 0.65165 / 0.33 (58006) hydrogen bonds : bond 0.04184 / 2.84 ( 1853) hydrogen bonds : angle 4.40417 / 3.14 ( 5207) Misc. bond : bond 0.00104 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 471 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7906 (tpp80) cc_final: 0.7440 (mmm-85) REVERT: A 286 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7996 (mtmm) REVERT: A 373 ARG cc_start: 0.8300 (ttm110) cc_final: 0.7841 (ttp80) REVERT: A 397 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6953 (mm-30) REVERT: B 34 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6962 (mm-30) REVERT: B 442 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.7179 (mmm160) REVERT: C 106 GLU cc_start: 0.8054 (tt0) cc_final: 0.7725 (mt-10) REVERT: C 279 GLU cc_start: 0.7647 (tp30) cc_final: 0.7390 (mm-30) REVERT: C 307 MET cc_start: 0.8584 (mmt) cc_final: 0.8068 (mmt) REVERT: C 368 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7442 (mm-30) REVERT: D 61 GLU cc_start: 0.8061 (tp30) cc_final: 0.7842 (tm-30) REVERT: D 163 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8671 (ttpp) REVERT: D 175 SER cc_start: 0.8170 (p) cc_final: 0.7935 (t) REVERT: D 232 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7690 (mm-40) REVERT: D 284 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: E 112 GLU cc_start: 0.7453 (tt0) cc_final: 0.7242 (tt0) REVERT: E 263 ASP cc_start: 0.7103 (t0) cc_final: 0.6832 (t0) REVERT: E 273 ASP cc_start: 0.7968 (t0) cc_final: 0.7767 (m-30) REVERT: E 302 MET cc_start: 0.8877 (mmm) cc_final: 0.8664 (mmp) REVERT: F 136 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: F 325 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8562 (ptp) REVERT: G 1235 ASN cc_start: 0.7288 (t0) cc_final: 0.7055 (t0) REVERT: G 1240 MET cc_start: 0.6015 (mmm) cc_final: 0.5630 (mpt) REVERT: G 1392 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: G 1429 ASN cc_start: 0.7855 (t0) cc_final: 0.7640 (t0) REVERT: G 1581 MET cc_start: 0.7252 (tpt) cc_final: 0.6936 (tpt) REVERT: H 455 MET cc_start: 0.8140 (mmm) cc_final: 0.7666 (mtm) REVERT: I 18 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7904 (mm-30) REVERT: I 167 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8092 (mttm) REVERT: J 174 GLU cc_start: 0.7817 (tt0) cc_final: 0.7578 (pt0) REVERT: J 635 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: J 677 ASP cc_start: 0.8090 (t0) cc_final: 0.7770 (t0) REVERT: N 91 LYS cc_start: 0.8139 (mttt) cc_final: 0.7619 (mmtt) REVERT: P 31 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6679 (tttm) REVERT: R 59 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7212 (ttmt) REVERT: R 85 ASP cc_start: 0.6476 (OUTLIER) cc_final: 0.6217 (t0) REVERT: R 92 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7239 (ttt-90) REVERT: R 95 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7319 (mtp-110) outliers start: 94 outliers final: 31 residues processed: 532 average time/residue: 0.9396 time to fit residues: 588.5251 Evaluate side-chains 480 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 436 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 208 TYR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1480 SER Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 92 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 426 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 449 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 243 optimal weight: 0.0000 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN B 168 GLN D 328 ASN E 328 ASN F 357 ASN G 989 GLN G1097 GLN I 199 ASN J 237 HIS J 259 ASN N 93 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS Q 93 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.108950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092367 restraints weight = 66266.704| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.54 r_work: 0.3249 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 42176 Z= 0.162 Angle : 0.667 31.137 58006 Z= 0.332 Chirality : 0.044 0.209 6607 Planarity : 0.004 0.054 6684 Dihedral : 21.380 163.199 7651 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.79 % Allowed : 14.47 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 4639 helix: 0.91 (0.11), residues: 2255 sheet: 0.22 (0.20), residues: 639 loop : 0.26 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 39 TYR 0.026 0.002 TYR G1591 PHE 0.016 0.002 PHE G1501 TRP 0.013 0.001 TRP G1036 HIS 0.007 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (42175) covalent geometry : angle 0.66696 / 0.33 (58006) hydrogen bonds : bond 0.04258 / 2.90 ( 1853) hydrogen bonds : angle 4.34881 / 3.11 ( 5207) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 455 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7380 (mmm-85) REVERT: A 170 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8769 (mttp) REVERT: A 286 LYS cc_start: 0.8299 (mtpp) cc_final: 0.7928 (mtmt) REVERT: A 373 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7800 (ttp80) REVERT: A 397 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6896 (mm-30) REVERT: B 34 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: B 442 ARG cc_start: 0.7512 (ttm-80) cc_final: 0.7154 (mmm160) REVERT: C 106 GLU cc_start: 0.7999 (tt0) cc_final: 0.7694 (mt-10) REVERT: C 307 MET cc_start: 0.8588 (mmt) cc_final: 0.8065 (mmt) REVERT: D 61 GLU cc_start: 0.8109 (tp30) cc_final: 0.7890 (tm-30) REVERT: D 90 MET cc_start: 0.8181 (mtp) cc_final: 0.7970 (mtp) REVERT: D 163 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8687 (ttpp) REVERT: D 175 SER cc_start: 0.8184 (p) cc_final: 0.7947 (t) REVERT: D 184 GLU cc_start: 0.8140 (tp30) cc_final: 0.7635 (tm-30) REVERT: D 228 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7996 (mm-30) REVERT: D 232 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7685 (mm-40) REVERT: D 284 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: E 61 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7886 (mm-30) REVERT: E 112 GLU cc_start: 0.7509 (tt0) cc_final: 0.7245 (tt0) REVERT: E 263 ASP cc_start: 0.7176 (t0) cc_final: 0.6836 (t0) REVERT: E 273 ASP cc_start: 0.7990 (t0) cc_final: 0.7773 (m-30) REVERT: E 302 MET cc_start: 0.8843 (mmm) cc_final: 0.8640 (mmp) REVERT: F 136 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: F 325 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8703 (ptp) REVERT: G 1145 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: G 1240 MET cc_start: 0.6050 (mmm) cc_final: 0.5657 (mpt) REVERT: G 1328 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8257 (mmmm) REVERT: G 1392 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7358 (m-30) REVERT: G 1581 MET cc_start: 0.7280 (tpt) cc_final: 0.6969 (tpt) REVERT: H 455 MET cc_start: 0.8209 (mmm) cc_final: 0.7727 (mtm) REVERT: I 167 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8119 (mttm) REVERT: J 174 GLU cc_start: 0.7856 (tt0) cc_final: 0.7620 (pt0) REVERT: J 295 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6326 (mtm-85) REVERT: J 626 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: J 635 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: J 677 ASP cc_start: 0.8084 (t0) cc_final: 0.7744 (t0) REVERT: M 133 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: N 84 MET cc_start: 0.7906 (tpp) cc_final: 0.7498 (tpt) REVERT: N 91 LYS cc_start: 0.8139 (mttt) cc_final: 0.7618 (mptt) REVERT: P 31 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6689 (tttm) REVERT: P 68 GLU cc_start: 0.7866 (tp30) cc_final: 0.7598 (tt0) REVERT: Q 65 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7694 (tt) REVERT: Q 79 LYS cc_start: 0.8153 (tmmt) cc_final: 0.7903 (tptp) REVERT: R 85 ASP cc_start: 0.6508 (OUTLIER) cc_final: 0.6279 (t0) REVERT: R 91 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8379 (ttmt) REVERT: R 92 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7210 (ttt-90) REVERT: R 95 ARG cc_start: 0.7932 (mtt90) cc_final: 0.7354 (mtp-110) outliers start: 105 outliers final: 44 residues processed: 526 average time/residue: 0.9357 time to fit residues: 583.2281 Evaluate side-chains 498 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 434 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 208 TYR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1085 SER Chi-restraints excluded: chain G residue 1145 GLU Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1328 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1480 SER Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1579 THR Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 92 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 55 optimal weight: 0.9980 chunk 339 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 472 optimal weight: 0.7980 chunk 393 optimal weight: 8.9990 chunk 206 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 449 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 443 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN C 146 ASN C 237 GLN C 409 GLN D 328 ASN E 328 ASN F 357 ASN G 989 GLN G1097 GLN I 199 ASN ** J 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 697 ASN J 722 GLN O 104 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.109212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092744 restraints weight = 66349.043| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.53 r_work: 0.3255 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42176 Z= 0.148 Angle : 0.653 31.047 58006 Z= 0.324 Chirality : 0.043 0.189 6607 Planarity : 0.004 0.054 6684 Dihedral : 21.287 157.683 7651 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.42 % Allowed : 15.95 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.12), residues: 4639 helix: 1.02 (0.11), residues: 2253 sheet: 0.20 (0.20), residues: 640 loop : 0.24 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 442 TYR 0.034 0.002 TYR P 80 PHE 0.026 0.001 PHE D 223 TRP 0.012 0.001 TRP J 287 HIS 0.006 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (42175) covalent geometry : angle 0.65301 / 0.32 (58006) hydrogen bonds : bond 0.04028 / 2.74 ( 1853) hydrogen bonds : angle 4.28172 / 3.05 ( 5207) Misc. bond : bond 0.00078 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 461 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7805 (tpp80) cc_final: 0.7367 (mmm-85) REVERT: A 170 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8775 (mttp) REVERT: A 286 LYS cc_start: 0.8326 (mtpp) cc_final: 0.7954 (mtmt) REVERT: A 373 ARG cc_start: 0.8293 (ttm110) cc_final: 0.7826 (ttp80) REVERT: B 34 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6958 (mm-30) REVERT: B 442 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7147 (mmm160) REVERT: C 106 GLU cc_start: 0.7940 (tt0) cc_final: 0.7636 (mt-10) REVERT: C 279 GLU cc_start: 0.7669 (tp30) cc_final: 0.7421 (mm-30) REVERT: D 61 GLU cc_start: 0.8098 (tp30) cc_final: 0.7885 (tm-30) REVERT: D 163 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8505 (ttpp) REVERT: D 175 SER cc_start: 0.8126 (p) cc_final: 0.7925 (t) REVERT: D 184 GLU cc_start: 0.8155 (tp30) cc_final: 0.7693 (tm-30) REVERT: D 228 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8038 (mm-30) REVERT: D 232 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7775 (mm-40) REVERT: D 284 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: E 61 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7928 (mm-30) REVERT: E 112 GLU cc_start: 0.7525 (tt0) cc_final: 0.7281 (tt0) REVERT: E 263 ASP cc_start: 0.7156 (t0) cc_final: 0.6789 (t0) REVERT: F 136 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: F 162 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8396 (tp) REVERT: F 284 GLU cc_start: 0.8142 (tp30) cc_final: 0.7896 (tp30) REVERT: F 325 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8697 (ptp) REVERT: G 1145 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7226 (mm-30) REVERT: G 1240 MET cc_start: 0.6120 (mmm) cc_final: 0.5727 (mpt) REVERT: G 1392 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: H 455 MET cc_start: 0.8160 (mmm) cc_final: 0.7718 (mtm) REVERT: I 167 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8105 (mttm) REVERT: J 174 GLU cc_start: 0.7850 (tt0) cc_final: 0.7626 (pt0) REVERT: J 635 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: J 677 ASP cc_start: 0.8130 (t0) cc_final: 0.7749 (t0) REVERT: N 84 MET cc_start: 0.7943 (tpp) cc_final: 0.7557 (tpt) REVERT: N 91 LYS cc_start: 0.8149 (mttt) cc_final: 0.7652 (mptt) REVERT: P 31 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6668 (tttm) REVERT: P 68 GLU cc_start: 0.7811 (tp30) cc_final: 0.7593 (tt0) REVERT: Q 65 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7673 (tt) REVERT: R 92 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7227 (ttt-90) REVERT: R 95 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7367 (mtp-110) outliers start: 91 outliers final: 35 residues processed: 524 average time/residue: 0.9628 time to fit residues: 594.2254 Evaluate side-chains 482 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 433 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 208 TYR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1145 GLU Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1579 THR Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 92 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 108 optimal weight: 6.9990 chunk 342 optimal weight: 1.9990 chunk 461 optimal weight: 5.9990 chunk 463 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 478 optimal weight: 1.9990 chunk 185 optimal weight: 0.0030 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN B 409 GLN D 328 ASN F 357 ASN F 419 GLN G 989 GLN G1097 GLN I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.109900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.093413 restraints weight = 66326.848| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.55 r_work: 0.3267 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42176 Z= 0.130 Angle : 0.640 30.821 58006 Z= 0.317 Chirality : 0.042 0.183 6607 Planarity : 0.004 0.055 6684 Dihedral : 21.112 158.146 7651 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.47 % Allowed : 16.54 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.12), residues: 4639 helix: 1.12 (0.11), residues: 2266 sheet: 0.20 (0.20), residues: 641 loop : 0.24 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 39 TYR 0.031 0.002 TYR P 80 PHE 0.015 0.001 PHE C 117 TRP 0.011 0.001 TRP G1650 HIS 0.009 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (42175) covalent geometry : angle 0.63987 / 0.32 (58006) hydrogen bonds : bond 0.03767 / 2.57 ( 1853) hydrogen bonds : angle 4.18900 / 2.99 ( 5207) Misc. bond : bond 0.00091 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 466 time to evaluate : 1.642 Fit side-chains revert: symmetry clash REVERT: A 170 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8747 (mttp) REVERT: A 187 GLN cc_start: 0.7760 (mt0) cc_final: 0.7525 (pt0) REVERT: A 286 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7911 (mtmt) REVERT: A 373 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7826 (ttp80) REVERT: B 34 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6907 (mm-30) REVERT: B 442 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7119 (mmm160) REVERT: C 106 GLU cc_start: 0.7944 (tt0) cc_final: 0.7668 (mt-10) REVERT: C 279 GLU cc_start: 0.7669 (tp30) cc_final: 0.7424 (mm-30) REVERT: C 307 MET cc_start: 0.8548 (mmt) cc_final: 0.8132 (mmt) REVERT: D 61 GLU cc_start: 0.8117 (tp30) cc_final: 0.7898 (tm-30) REVERT: D 90 MET cc_start: 0.8014 (mtp) cc_final: 0.7777 (mtp) REVERT: D 163 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8709 (ttpp) REVERT: D 228 GLU cc_start: 0.8235 (mt-10) cc_final: 0.8024 (mm-30) REVERT: E 61 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7920 (mm-30) REVERT: E 112 GLU cc_start: 0.7531 (tt0) cc_final: 0.7323 (tt0) REVERT: E 263 ASP cc_start: 0.7139 (t0) cc_final: 0.6750 (t0) REVERT: E 359 HIS cc_start: 0.7287 (m-70) cc_final: 0.7023 (p-80) REVERT: F 136 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: F 263 ASP cc_start: 0.7077 (t0) cc_final: 0.6823 (t0) REVERT: F 284 GLU cc_start: 0.8152 (tp30) cc_final: 0.7874 (tp30) REVERT: F 325 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8696 (ptp) REVERT: G 1235 ASN cc_start: 0.7532 (t0) cc_final: 0.7215 (t0) REVERT: G 1240 MET cc_start: 0.6111 (mmm) cc_final: 0.5733 (mpt) REVERT: G 1312 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: G 1392 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: H 455 MET cc_start: 0.8153 (mmm) cc_final: 0.7749 (mtm) REVERT: H 464 GLU cc_start: 0.8036 (mp0) cc_final: 0.7413 (mp0) REVERT: I 167 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8094 (mttm) REVERT: J 225 LEU cc_start: 0.8577 (mt) cc_final: 0.8368 (mp) REVERT: J 626 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: J 635 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: J 677 ASP cc_start: 0.8163 (t0) cc_final: 0.7822 (t0) REVERT: N 84 MET cc_start: 0.7845 (tpp) cc_final: 0.7392 (tpt) REVERT: N 91 LYS cc_start: 0.8167 (mttt) cc_final: 0.7616 (mptt) REVERT: P 31 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6660 (tmtm) REVERT: P 82 LYS cc_start: 0.7944 (mtmm) cc_final: 0.7560 (mttm) REVERT: Q 65 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7639 (tt) REVERT: Q 133 GLU cc_start: 0.6642 (tt0) cc_final: 0.6230 (mt-10) REVERT: R 91 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8423 (ttmt) REVERT: R 95 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7363 (mtp-110) outliers start: 93 outliers final: 42 residues processed: 529 average time/residue: 0.9383 time to fit residues: 585.5602 Evaluate side-chains 478 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 423 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1198 MET Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1312 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1579 THR Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 91 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 154 optimal weight: 2.9990 chunk 329 optimal weight: 0.9980 chunk 443 optimal weight: 2.9990 chunk 342 optimal weight: 0.6980 chunk 380 optimal weight: 5.9990 chunk 326 optimal weight: 4.9990 chunk 422 optimal weight: 9.9990 chunk 224 optimal weight: 0.1980 chunk 165 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN C 146 ASN D 328 ASN E 96 GLN F 357 ASN I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN ** R 25 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 = 0.3648 r_free = 0.3648 target = 0.110227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093899 restraints weight = 66184.002| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.53 r_work: 0.3276 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42176 Z= 0.127 Angle : 0.642 30.868 58006 Z= 0.317 Chirality : 0.042 0.200 6607 Planarity : 0.004 0.062 6684 Dihedral : 20.987 158.366 7651 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.02 % Allowed : 17.95 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.12), residues: 4639 helix: 1.24 (0.11), residues: 2256 sheet: 0.21 (0.20), residues: 640 loop : 0.24 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G1234 TYR 0.021 0.001 TYR J 167 PHE 0.028 0.001 PHE D 223 TRP 0.015 0.001 TRP G1036 HIS 0.006 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (42175) covalent geometry : angle 0.64223 / 0.32 (58006) hydrogen bonds : bond 0.03635 / 2.48 ( 1853) hydrogen bonds : angle 4.13693 / 2.94 ( 5207) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 448 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7622 (tpp80) cc_final: 0.7246 (mmm-85) REVERT: A 286 LYS cc_start: 0.8341 (mtpp) cc_final: 0.7955 (mtmt) REVERT: A 373 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7836 (ttp80) REVERT: B 34 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6915 (mm-30) REVERT: B 442 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7190 (mmm160) REVERT: C 106 GLU cc_start: 0.7902 (tt0) cc_final: 0.7634 (mt-10) REVERT: D 61 GLU cc_start: 0.8132 (tp30) cc_final: 0.7927 (tm-30) REVERT: D 90 MET cc_start: 0.8059 (mtp) cc_final: 0.7803 (mtp) REVERT: D 163 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8668 (ttpp) REVERT: D 184 GLU cc_start: 0.8072 (tp30) cc_final: 0.7725 (tm-30) REVERT: E 61 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7925 (mm-30) REVERT: E 263 ASP cc_start: 0.7169 (t0) cc_final: 0.6827 (t70) REVERT: E 359 HIS cc_start: 0.7303 (m-70) cc_final: 0.7077 (p-80) REVERT: F 136 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: F 263 ASP cc_start: 0.7056 (t0) cc_final: 0.6815 (t0) REVERT: F 284 GLU cc_start: 0.8102 (tp30) cc_final: 0.7836 (tp30) REVERT: F 313 ARG cc_start: 0.7585 (tpp-160) cc_final: 0.7351 (tpp-160) REVERT: F 325 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8702 (ptp) REVERT: G 1145 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: G 1240 MET cc_start: 0.6166 (mmm) cc_final: 0.5811 (mpt) REVERT: G 1392 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: G 1581 MET cc_start: 0.7194 (tpt) cc_final: 0.6951 (tpt) REVERT: H 455 MET cc_start: 0.8072 (mmm) cc_final: 0.7703 (mtm) REVERT: H 463 GLU cc_start: 0.7340 (pm20) cc_final: 0.7067 (pm20) REVERT: H 464 GLU cc_start: 0.8095 (mp0) cc_final: 0.7871 (mp0) REVERT: J 225 LEU cc_start: 0.8603 (mt) cc_final: 0.8388 (mp) REVERT: J 626 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: J 635 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6884 (pm20) REVERT: J 677 ASP cc_start: 0.8131 (t0) cc_final: 0.7876 (t0) REVERT: N 84 MET cc_start: 0.7887 (tpp) cc_final: 0.7415 (tpt) REVERT: N 91 LYS cc_start: 0.8209 (mttt) cc_final: 0.7692 (mptt) REVERT: P 68 GLU cc_start: 0.7868 (tp30) cc_final: 0.7610 (tt0) REVERT: P 73 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7452 (tp30) REVERT: Q 65 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7600 (tt) REVERT: Q 118 THR cc_start: 0.6582 (OUTLIER) cc_final: 0.6353 (t) REVERT: Q 133 GLU cc_start: 0.6598 (tt0) cc_final: 0.6270 (mt-10) REVERT: R 95 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7399 (mtp-110) outliers start: 76 outliers final: 38 residues processed: 496 average time/residue: 0.8799 time to fit residues: 517.3869 Evaluate side-chains 475 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 427 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1145 GLU Chi-restraints excluded: chain G residue 1198 MET Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1579 THR Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 75 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 133 optimal weight: 0.8980 chunk 233 optimal weight: 8.9990 chunk 439 optimal weight: 3.9990 chunk 471 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 472 optimal weight: 6.9990 chunk 434 optimal weight: 0.9990 chunk 25 optimal weight: 0.0370 chunk 175 optimal weight: 1.9990 chunk 381 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 328 ASN F 357 ASN G1235 ASN I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 633 ASN Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.109658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093176 restraints weight = 66523.909| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.55 r_work: 0.3262 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42176 Z= 0.143 Angle : 0.656 31.242 58006 Z= 0.323 Chirality : 0.042 0.185 6607 Planarity : 0.004 0.054 6684 Dihedral : 20.968 158.784 7651 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.78 % Allowed : 18.37 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.12), residues: 4639 helix: 1.21 (0.11), residues: 2259 sheet: 0.20 (0.20), residues: 638 loop : 0.21 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G1234 TYR 0.020 0.002 TYR E 339 PHE 0.015 0.001 PHE G1501 TRP 0.013 0.001 TRP G1036 HIS 0.005 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (42175) covalent geometry : angle 0.65560 / 0.32 (58006) hydrogen bonds : bond 0.03766 / 2.57 ( 1853) hydrogen bonds : angle 4.16216 / 2.96 ( 5207) Misc. bond : bond 0.00072 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 440 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7765 (tpp80) cc_final: 0.7327 (mmm-85) REVERT: A 286 LYS cc_start: 0.8335 (mtpp) cc_final: 0.7923 (mtmt) REVERT: A 373 ARG cc_start: 0.8284 (ttm110) cc_final: 0.7825 (ttp80) REVERT: B 34 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6921 (mm-30) REVERT: B 442 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.7158 (mmm160) REVERT: C 62 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5579 (ppp) REVERT: C 106 GLU cc_start: 0.7929 (tt0) cc_final: 0.7663 (mt-10) REVERT: C 327 ILE cc_start: 0.8568 (tt) cc_final: 0.8233 (tt) REVERT: D 61 GLU cc_start: 0.8133 (tp30) cc_final: 0.7925 (tm-30) REVERT: D 90 MET cc_start: 0.8094 (mtp) cc_final: 0.7841 (mtp) REVERT: D 163 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8677 (ttpp) REVERT: D 184 GLU cc_start: 0.8082 (tp30) cc_final: 0.7767 (tm-30) REVERT: D 228 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8026 (mm-30) REVERT: D 395 GLU cc_start: 0.8057 (pt0) cc_final: 0.7646 (tt0) REVERT: E 61 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7862 (mm-30) REVERT: F 136 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: F 263 ASP cc_start: 0.7084 (t0) cc_final: 0.6824 (t0) REVERT: F 284 GLU cc_start: 0.8111 (tp30) cc_final: 0.7825 (tp30) REVERT: F 325 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8713 (ptp) REVERT: G 1018 TYR cc_start: 0.7072 (m-10) cc_final: 0.6681 (m-10) REVERT: G 1145 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: G 1240 MET cc_start: 0.6195 (mmm) cc_final: 0.5846 (mpt) REVERT: G 1312 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: G 1392 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: H 455 MET cc_start: 0.8140 (mmm) cc_final: 0.7768 (mtm) REVERT: H 464 GLU cc_start: 0.8034 (mp0) cc_final: 0.7784 (mp0) REVERT: J 17 GLU cc_start: 0.5648 (pm20) cc_final: 0.4970 (pp20) REVERT: J 225 LEU cc_start: 0.8606 (mt) cc_final: 0.8404 (mp) REVERT: J 626 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: J 635 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: J 677 ASP cc_start: 0.8129 (t0) cc_final: 0.7857 (t0) REVERT: N 84 MET cc_start: 0.7850 (tpp) cc_final: 0.7477 (tpp) REVERT: N 91 LYS cc_start: 0.8182 (mttt) cc_final: 0.7643 (mptt) REVERT: P 68 GLU cc_start: 0.7855 (tp30) cc_final: 0.7586 (tt0) REVERT: P 82 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7408 (mttm) REVERT: Q 65 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7601 (tt) REVERT: Q 133 GLU cc_start: 0.6614 (tt0) cc_final: 0.6270 (mt-10) REVERT: R 95 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7382 (mtp-110) outliers start: 67 outliers final: 43 residues processed: 484 average time/residue: 0.8663 time to fit residues: 496.2886 Evaluate side-chains 475 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 421 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1085 SER Chi-restraints excluded: chain G residue 1145 GLU Chi-restraints excluded: chain G residue 1198 MET Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1312 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1579 THR Chi-restraints excluded: chain G residue 1691 LEU Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 75 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 119 optimal weight: 0.9980 chunk 390 optimal weight: 30.0000 chunk 445 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 429 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 366 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 324 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 328 ASN E 96 GLN F 357 ASN G1235 ASN I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.109331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092919 restraints weight = 65956.302| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.53 r_work: 0.3257 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 42176 Z= 0.153 Angle : 0.670 31.481 58006 Z= 0.330 Chirality : 0.043 0.263 6607 Planarity : 0.005 0.065 6684 Dihedral : 20.962 159.375 7651 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.65 % Allowed : 18.90 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.12), residues: 4639 helix: 1.19 (0.11), residues: 2258 sheet: 0.17 (0.20), residues: 638 loop : 0.19 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Q 129 TYR 0.027 0.002 TYR N 88 PHE 0.029 0.001 PHE D 223 TRP 0.013 0.001 TRP G1036 HIS 0.005 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (42175) covalent geometry : angle 0.67003 / 0.33 (58006) hydrogen bonds : bond 0.03825 / 2.61 ( 1853) hydrogen bonds : angle 4.17232 / 2.97 ( 5207) Misc. bond : bond 0.00064 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 431 time to evaluate : 1.649 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7692 (tpp80) cc_final: 0.7358 (mmm-85) REVERT: A 286 LYS cc_start: 0.8338 (mtpp) cc_final: 0.7930 (mtmt) REVERT: A 373 ARG cc_start: 0.8287 (ttm110) cc_final: 0.7827 (ttp80) REVERT: A 401 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7131 (mtm180) REVERT: B 34 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: B 421 ASN cc_start: 0.8000 (m-40) cc_final: 0.7795 (m110) REVERT: B 442 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7146 (mmm160) REVERT: C 62 MET cc_start: 0.5792 (OUTLIER) cc_final: 0.5500 (ppp) REVERT: C 106 GLU cc_start: 0.7954 (tt0) cc_final: 0.7737 (mt-10) REVERT: C 327 ILE cc_start: 0.8607 (tt) cc_final: 0.8282 (tt) REVERT: D 61 GLU cc_start: 0.8157 (tp30) cc_final: 0.7944 (tm-30) REVERT: D 90 MET cc_start: 0.8130 (mtp) cc_final: 0.7890 (mtp) REVERT: D 163 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8672 (ttpp) REVERT: D 184 GLU cc_start: 0.8112 (tp30) cc_final: 0.7751 (tm-30) REVERT: D 228 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8018 (mm-30) REVERT: D 302 MET cc_start: 0.8373 (mmp) cc_final: 0.8118 (mmm) REVERT: D 395 GLU cc_start: 0.8068 (pt0) cc_final: 0.7701 (tt0) REVERT: E 61 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7902 (mm-30) REVERT: E 378 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7013 (mm-30) REVERT: F 136 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: F 263 ASP cc_start: 0.7014 (t0) cc_final: 0.6741 (t0) REVERT: F 284 GLU cc_start: 0.8089 (tp30) cc_final: 0.7813 (tp30) REVERT: G 1145 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: G 1240 MET cc_start: 0.6236 (mmm) cc_final: 0.5854 (mpt) REVERT: G 1312 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: G 1392 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: H 455 MET cc_start: 0.8108 (mmm) cc_final: 0.7720 (mtm) REVERT: H 463 GLU cc_start: 0.7473 (pm20) cc_final: 0.7134 (pm20) REVERT: I 22 LEU cc_start: 0.8557 (mp) cc_final: 0.8159 (tp) REVERT: J 17 GLU cc_start: 0.5800 (pm20) cc_final: 0.5198 (pp20) REVERT: J 626 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: J 635 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6869 (pm20) REVERT: J 677 ASP cc_start: 0.8127 (t0) cc_final: 0.7844 (t0) REVERT: N 84 MET cc_start: 0.7959 (tpp) cc_final: 0.7740 (tpp) REVERT: N 91 LYS cc_start: 0.8193 (mttt) cc_final: 0.7653 (mptt) REVERT: O 20 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7876 (mtp180) REVERT: P 68 GLU cc_start: 0.7804 (tp30) cc_final: 0.7505 (tt0) REVERT: Q 65 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7605 (tt) REVERT: Q 133 GLU cc_start: 0.6642 (tt0) cc_final: 0.6268 (mt-10) REVERT: R 95 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7381 (mtp-110) outliers start: 62 outliers final: 42 residues processed: 469 average time/residue: 0.8764 time to fit residues: 487.3933 Evaluate side-chains 475 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 421 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1085 SER Chi-restraints excluded: chain G residue 1145 GLU Chi-restraints excluded: chain G residue 1198 MET Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1312 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1579 THR Chi-restraints excluded: chain G residue 1691 LEU Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 20 ARG Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 75 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 166 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 402 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 340 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 305 optimal weight: 5.9990 chunk 342 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 146 ASN D 328 ASN F 357 ASN G1235 ASN I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.110159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094638 restraints weight = 66371.641| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.53 r_work: 0.3269 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 42176 Z= 0.129 Angle : 0.647 30.945 58006 Z= 0.318 Chirality : 0.042 0.234 6607 Planarity : 0.004 0.078 6684 Dihedral : 20.856 159.591 7651 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.57 % Allowed : 19.19 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.12), residues: 4639 helix: 1.31 (0.11), residues: 2245 sheet: 0.19 (0.20), residues: 639 loop : 0.25 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG Q 129 TYR 0.057 0.002 TYR P 80 PHE 0.027 0.001 PHE D 223 TRP 0.024 0.001 TRP G1036 HIS 0.005 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (42175) covalent geometry : angle 0.64667 / 0.32 (58006) hydrogen bonds : bond 0.03581 / 2.45 ( 1853) hydrogen bonds : angle 4.11035 / 2.92 ( 5207) Misc. bond : bond 0.00074 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19505.26 seconds wall clock time: 331 minutes 24.42 seconds (19884.42 seconds total)