Starting phenix.real_space_refine on Wed Feb 21 02:55:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2024/7var_31860_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2024/7var_31860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2024/7var_31860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2024/7var_31860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2024/7var_31860_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2024/7var_31860_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18720 2.51 5 N 5125 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29520 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4467 Classifications: {'peptide': 577} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain breaks: 1 Chain: "C" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 981 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" 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: 15.88, per 1000 atoms: 0.54 Number of scatterers: 29520 At special positions: 0 Unit cell: (140.8, 174.24, 150.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 5 15.00 Mg 2 11.99 O 5565 8.00 N 5125 7.00 C 18720 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.69 Conformation dependent library (CDL) restraints added in 5.4 seconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 36 sheets defined 42.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.00 Creating SS restraints... Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 315 removed outlier: 4.101A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.004A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.970A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.975A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 574 removed outlier: 3.678A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.738A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 364 removed outlier: 4.304A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 470 removed outlier: 3.783A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 531 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.688A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.501A pdb=" N ARG B 550 " --> pdb=" O ARG B 547 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG B 552 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 575 removed outlier: 3.612A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 271 removed outlier: 3.643A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 3.885A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 340 Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.892A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.690A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.523A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.164A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 531 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 556 through 577 Proline residue: C 560 - end of helix removed outlier: 3.749A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 228 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 297 removed outlier: 4.504A pdb=" N ARG D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.564A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 395 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.989A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 470 through 472 No H-bonds generated for 'chain 'D' and resid 470 through 472' Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 136 through 141 removed outlier: 3.616A pdb=" N MET E 141 " --> pdb=" O THR E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.646A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 285 through 297 removed outlier: 4.479A pdb=" N TYR E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU E 296 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E 297 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 362 through 365 No H-bonds generated for 'chain 'E' and resid 362 through 365' Processing helix chain 'E' and resid 375 through 399 removed outlier: 4.193A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 443 Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 458 through 461 No H-bonds generated for 'chain 'E' and resid 458 through 461' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.552A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 90' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 229 through 249 removed outlier: 3.776A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.595A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.734A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 346 removed outlier: 3.512A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 375 through 398 removed outlier: 3.527A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.891A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'F' and resid 467 through 470 No H-bonds generated for 'chain 'F' and resid 467 through 470' Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.913A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 111 through 114 Processing helix chain 'G' and resid 121 through 207 removed outlier: 3.582A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 7 through 15 Processing helix chain 'H' and resid 26 through 39 Processing helix chain 'H' and resid 55 through 58 Processing helix chain 'H' and resid 77 through 80 No H-bonds generated for 'chain 'H' and resid 77 through 80' Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 84 through 118 removed outlier: 3.828A pdb=" N TYR I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 92 Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 100 through 114 Processing helix chain 'J' and resid 125 through 130 Proline residue: J 129 - end of helix No H-bonds generated for 'chain 'J' and resid 125 through 130' Processing helix chain 'J' and resid 132 through 138 Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.523A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 4.472A pdb=" N LEU K 85 " --> pdb=" O GLU K 82 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA K 86 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG K 87 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA K 105 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG K 106 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU K 107 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASP K 108 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS K 116 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL K 118 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 94 through 96 No H-bonds generated for 'chain 'L' and resid 94 through 96' Processing helix chain 'L' and resid 100 through 114 Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 4.715A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 4.578A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.456A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.555A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.740A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 223 through 227 removed outlier: 6.562A pdb=" N ILE A 380 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE A 226 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY A 382 " --> pdb=" O ILE A 226 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.735A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.046A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.343A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= J, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.624A pdb=" N GLY B 164 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 405 through 407 removed outlier: 8.748A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 366 through 369 Processing sheet with id= M, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.520A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 157 through 160 removed outlier: 7.011A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.642A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= Q, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= R, first strand: chain 'C' and resid 223 through 227 removed outlier: 8.576A pdb=" N ALA C 224 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 380 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE C 226 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY C 382 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 249 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N MET C 323 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= T, first strand: chain 'C' and resid 134 through 140 removed outlier: 6.663A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.828A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.445A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.621A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.950A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N MET D 194 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Z, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.601A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU E 77 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.384A pdb=" N PHE E 93 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU E 219 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AC, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.564A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.688A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.971A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AG, first strand: chain 'G' and resid 89 through 96 Processing sheet with id= AH, first strand: chain 'H' and resid 19 through 22 Processing sheet with id= AI, first strand: chain 'J' and resid 141 through 144 removed outlier: 3.748A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.595A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.90 Time building geometry restraints manager: 12.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9966 1.34 - 1.46: 5196 1.46 - 1.58: 14709 1.58 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30074 Sorted by residual: bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C5 ADP A 601 " pdb=" C6 ADP A 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.590 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" N ARG F 372 " pdb=" CA ARG F 372 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.87e+00 bond pdb=" N GLU D 296 " pdb=" CA GLU D 296 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.30e-02 5.92e+03 8.14e+00 ... (remaining 30069 not shown) Histogram of bond angle deviations from ideal: 100.06 - 108.00: 1258 108.00 - 115.94: 18470 115.94 - 123.87: 20299 123.87 - 131.81: 685 131.81 - 139.75: 42 Bond angle restraints: 40754 Sorted by residual: angle pdb=" PA ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 120.50 136.72 -16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O2B ADP A 601 " ideal model delta sigma weight residual 119.90 106.99 12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" N THR G 119 " pdb=" CA THR G 119 " pdb=" C THR G 119 " ideal model delta sigma weight residual 109.81 117.95 -8.14 2.21e+00 2.05e-01 1.36e+01 angle pdb=" CA ALA D 298 " pdb=" C ALA D 298 " pdb=" O ALA D 298 " ideal model delta sigma weight residual 121.56 117.98 3.58 1.09e+00 8.42e-01 1.08e+01 angle pdb=" C ALA E 441 " pdb=" N LEU E 442 " pdb=" CA LEU E 442 " ideal model delta sigma weight residual 122.06 116.03 6.03 1.86e+00 2.89e-01 1.05e+01 ... (remaining 40749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.89: 17752 27.89 - 55.78: 511 55.78 - 83.67: 74 83.67 - 111.56: 10 111.56 - 139.45: 2 Dihedral angle restraints: 18349 sinusoidal: 7531 harmonic: 10818 Sorted by residual: dihedral pdb=" O2A ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PA ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 79.45 -139.45 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 78.40 -138.41 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" C THR F 371 " pdb=" N THR F 371 " pdb=" CA THR F 371 " pdb=" CB THR F 371 " ideal model delta harmonic sigma weight residual -122.00 -137.73 15.73 0 2.50e+00 1.60e-01 3.96e+01 ... (remaining 18346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 4331 0.095 - 0.191: 235 0.191 - 0.286: 0 0.286 - 0.381: 0 0.381 - 0.477: 1 Chirality restraints: 4567 Sorted by residual: chirality pdb=" CA THR F 371 " pdb=" N THR F 371 " pdb=" C THR F 371 " pdb=" CB THR F 371 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 4564 not shown) Planarity restraints: 5336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 124 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO L 125 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO L 125 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 125 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 101 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO G 102 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 102 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 102 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO E 324 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " -0.023 5.00e-02 4.00e+02 ... (remaining 5333 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 168 2.61 - 3.18: 25203 3.18 - 3.76: 44611 3.76 - 4.33: 63399 4.33 - 4.90: 106632 Nonbonded interactions: 240013 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 2.038 2.170 nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.065 2.170 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLU H 28 " model vdw 2.145 2.440 nonbonded pdb=" OD1 ASP F 34 " pdb=" OG SER F 74 " model vdw 2.216 2.440 nonbonded pdb=" OH TYR D 263 " pdb=" OD2 ASP D 290 " model vdw 2.228 2.440 ... (remaining 240008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 32 or resid 34 through 578)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 32 or resid 34 through 578)) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.570 Check model and map are aligned: 0.470 Set scattering table: 0.240 Process input model: 76.770 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.170 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:10.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 30074 Z= 0.183 Angle : 0.556 16.222 40754 Z= 0.308 Chirality : 0.043 0.477 4567 Planarity : 0.004 0.059 5336 Dihedral : 13.345 139.447 11433 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.06 % Allowed : 0.26 % Favored : 99.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.14), residues: 3761 helix: 1.89 (0.14), residues: 1554 sheet: 0.35 (0.22), residues: 579 loop : 0.42 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 119 HIS 0.003 0.001 HIS F 252 PHE 0.009 0.001 PHE B 143 TYR 0.010 0.001 TYR G 133 ARG 0.008 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 507 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8104 (ptpp) cc_final: 0.7625 (mttp) REVERT: A 143 PHE cc_start: 0.8529 (m-80) cc_final: 0.8188 (m-10) REVERT: A 154 ARG cc_start: 0.7613 (ptm160) cc_final: 0.7105 (ptt90) REVERT: A 445 GLU cc_start: 0.7852 (tp30) cc_final: 0.7442 (tp30) REVERT: A 502 GLU cc_start: 0.7829 (pm20) cc_final: 0.7395 (mp0) REVERT: A 524 LYS cc_start: 0.7697 (mmtp) cc_final: 0.7412 (ptmt) REVERT: A 546 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6668 (mm-30) REVERT: A 547 ARG cc_start: 0.7529 (ttm-80) cc_final: 0.7127 (ttm110) REVERT: B 38 GLU cc_start: 0.7968 (tt0) cc_final: 0.7610 (tt0) REVERT: B 130 ARG cc_start: 0.7341 (mmt-90) cc_final: 0.7077 (mpt180) REVERT: B 467 ILE cc_start: 0.6882 (mm) cc_final: 0.6523 (mt) REVERT: B 502 GLU cc_start: 0.8006 (tt0) cc_final: 0.7764 (mp0) REVERT: C 121 PRO cc_start: 0.8976 (Cg_endo) cc_final: 0.8775 (Cg_exo) REVERT: C 140 GLU cc_start: 0.7594 (tp30) cc_final: 0.7215 (tt0) REVERT: C 488 ARG cc_start: 0.7943 (tmm-80) cc_final: 0.7577 (ttp-170) REVERT: C 546 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7397 (pt0) REVERT: C 550 ARG cc_start: 0.7615 (ttp-110) cc_final: 0.6888 (ttm-80) REVERT: D 74 SER cc_start: 0.8315 (t) cc_final: 0.8100 (m) REVERT: D 275 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7718 (mt-10) REVERT: D 453 ARG cc_start: 0.7418 (mtp85) cc_final: 0.7153 (mtp85) REVERT: E 196 ILE cc_start: 0.8083 (mm) cc_final: 0.7393 (pt) REVERT: E 206 GLN cc_start: 0.7360 (mt0) cc_final: 0.7136 (mp10) REVERT: E 274 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7207 (mtm-85) REVERT: E 410 ARG cc_start: 0.6981 (ttm110) cc_final: 0.6770 (ttt90) REVERT: F 98 LYS cc_start: 0.7501 (mmtm) cc_final: 0.7214 (mmpt) REVERT: F 128 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7376 (mm-30) REVERT: F 178 SER cc_start: 0.8043 (t) cc_final: 0.7735 (p) REVERT: F 210 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7704 (ttm170) REVERT: G 30 LYS cc_start: 0.7502 (mtpp) cc_final: 0.7260 (mttt) REVERT: G 38 GLU cc_start: 0.6987 (tt0) cc_final: 0.6361 (tp30) REVERT: G 96 VAL cc_start: 0.7218 (t) cc_final: 0.6973 (m) REVERT: G 149 LYS cc_start: 0.7259 (mmtt) cc_final: 0.6709 (mtmt) REVERT: H 19 GLU cc_start: 0.4165 (tt0) cc_final: 0.3625 (tp30) REVERT: H 28 GLU cc_start: 0.4253 (pm20) cc_final: 0.3946 (tt0) REVERT: J 122 VAL cc_start: 0.6143 (t) cc_final: 0.5764 (p) REVERT: J 134 LEU cc_start: 0.4500 (pt) cc_final: 0.3618 (mp) REVERT: K 91 ARG cc_start: 0.4595 (ttm170) cc_final: 0.4266 (mtp85) REVERT: K 104 MET cc_start: 0.5725 (ttm) cc_final: 0.5203 (ttp) REVERT: L 105 ARG cc_start: 0.6833 (mtm-85) cc_final: 0.6497 (mtm-85) REVERT: L 119 LYS cc_start: 0.7084 (pttt) cc_final: 0.6746 (pttp) REVERT: L 172 ASP cc_start: 0.7519 (m-30) cc_final: 0.7155 (t0) REVERT: L 181 LYS cc_start: 0.6696 (mmmt) cc_final: 0.6395 (mttm) REVERT: L 187 TRP cc_start: 0.6663 (m-90) cc_final: 0.6377 (m-90) outliers start: 2 outliers final: 1 residues processed: 509 average time/residue: 1.9042 time to fit residues: 1094.5041 Evaluate side-chains 293 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 363 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 338 optimal weight: 0.5980 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 541 GLN A 571 GLN B 202 ASN B 260 ASN B 423 ASN C 238 GLN F 206 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 181 GLN L 165 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 30074 Z= 0.386 Angle : 0.631 8.883 40754 Z= 0.326 Chirality : 0.048 0.183 4567 Planarity : 0.006 0.063 5336 Dihedral : 6.671 145.013 4232 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.24 % Allowed : 8.83 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3761 helix: 1.11 (0.13), residues: 1542 sheet: 0.25 (0.22), residues: 558 loop : 0.20 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 119 HIS 0.009 0.001 HIS L 130 PHE 0.015 0.002 PHE D 191 TYR 0.017 0.002 TYR B 304 ARG 0.006 0.001 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 292 time to evaluate : 3.378 Fit side-chains revert: symmetry clash REVERT: A 154 ARG cc_start: 0.7611 (ptm160) cc_final: 0.7062 (ptt90) REVERT: A 197 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.7321 (ttp80) REVERT: A 323 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7346 (mtt) REVERT: A 342 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: A 441 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6892 (tt0) REVERT: A 445 GLU cc_start: 0.7783 (tp30) cc_final: 0.7297 (tp30) REVERT: A 502 GLU cc_start: 0.7785 (pm20) cc_final: 0.7372 (mp0) REVERT: A 524 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7387 (ptmt) REVERT: A 547 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.6900 (ttm110) REVERT: B 38 GLU cc_start: 0.8012 (tt0) cc_final: 0.7640 (tt0) REVERT: B 170 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7181 (tp30) REVERT: B 314 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7277 (ptt90) REVERT: B 408 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7454 (ttt-90) REVERT: B 410 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: B 467 ILE cc_start: 0.6840 (mm) cc_final: 0.6529 (mt) REVERT: B 502 GLU cc_start: 0.8008 (tt0) cc_final: 0.7760 (mp0) REVERT: B 567 MET cc_start: 0.7356 (tpt) cc_final: 0.7145 (tpt) REVERT: B 571 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6405 (mp10) REVERT: C 54 ASP cc_start: 0.7643 (t0) cc_final: 0.7198 (t0) REVERT: C 128 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: C 323 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7250 (mmt) REVERT: C 441 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: C 532 ARG cc_start: 0.5717 (OUTLIER) cc_final: 0.5403 (mtp85) REVERT: C 546 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7167 (pt0) REVERT: C 550 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7001 (ttm-80) REVERT: D 25 LYS cc_start: 0.8310 (ptpt) cc_final: 0.7852 (mtpt) REVERT: D 206 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7051 (mp10) REVERT: D 269 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6998 (mt-10) REVERT: D 275 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7789 (mt-10) REVERT: E 34 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7371 (t0) REVERT: E 162 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: E 206 GLN cc_start: 0.7345 (mt0) cc_final: 0.7055 (mp10) REVERT: E 334 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7654 (mm-30) REVERT: F 162 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: F 210 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7703 (ttm170) REVERT: F 373 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7320 (pt0) REVERT: F 391 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: G 13 GLN cc_start: 0.8260 (tm-30) cc_final: 0.8029 (tp40) REVERT: G 38 GLU cc_start: 0.7123 (tt0) cc_final: 0.6329 (tp30) REVERT: G 68 GLN cc_start: 0.2407 (OUTLIER) cc_final: 0.2203 (tp40) REVERT: G 137 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6971 (mt) REVERT: G 149 LYS cc_start: 0.7302 (mmtt) cc_final: 0.6878 (mppt) REVERT: H 91 ARG cc_start: 0.6516 (mmm160) cc_final: 0.5741 (mmp80) REVERT: J 122 VAL cc_start: 0.6166 (t) cc_final: 0.5954 (p) REVERT: J 134 LEU cc_start: 0.4213 (pt) cc_final: 0.3618 (mp) REVERT: J 148 LEU cc_start: 0.2923 (tp) cc_final: 0.2371 (pp) REVERT: J 172 ASP cc_start: 0.5569 (m-30) cc_final: 0.5349 (m-30) REVERT: K 91 ARG cc_start: 0.4603 (ttm170) cc_final: 0.4332 (mtp85) REVERT: K 104 MET cc_start: 0.5661 (ttm) cc_final: 0.5381 (ttp) REVERT: K 106 ARG cc_start: 0.7106 (mtm-85) cc_final: 0.6323 (mtt90) REVERT: L 119 LYS cc_start: 0.7046 (pttt) cc_final: 0.6814 (pttp) REVERT: L 165 ASN cc_start: 0.7310 (t0) cc_final: 0.7050 (t160) outliers start: 69 outliers final: 14 residues processed: 344 average time/residue: 2.0133 time to fit residues: 782.9982 Evaluate side-chains 287 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 253 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain H residue 33 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 281 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 339 optimal weight: 5.9990 chunk 366 optimal weight: 9.9990 chunk 302 optimal weight: 4.9990 chunk 336 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 272 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN B 477 GLN D 364 ASN E 58 GLN F 310 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30074 Z= 0.315 Angle : 0.574 9.726 40754 Z= 0.295 Chirality : 0.046 0.176 4567 Planarity : 0.005 0.049 5336 Dihedral : 6.628 151.109 4230 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.14 % Allowed : 11.16 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3761 helix: 0.98 (0.14), residues: 1542 sheet: 0.13 (0.21), residues: 578 loop : 0.11 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 97 HIS 0.009 0.001 HIS L 130 PHE 0.015 0.002 PHE A 230 TYR 0.013 0.001 TYR F 203 ARG 0.008 0.000 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 276 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8188 (ptpp) cc_final: 0.7591 (mttp) REVERT: A 143 PHE cc_start: 0.8691 (m-80) cc_final: 0.8356 (m-10) REVERT: A 154 ARG cc_start: 0.7659 (ptm160) cc_final: 0.7043 (ptt90) REVERT: A 197 ARG cc_start: 0.7550 (ttp-110) cc_final: 0.7321 (ttp80) REVERT: A 323 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7301 (mtt) REVERT: A 342 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: A 441 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: A 502 GLU cc_start: 0.7835 (pm20) cc_final: 0.7435 (mp0) REVERT: A 524 LYS cc_start: 0.7764 (mmtp) cc_final: 0.7432 (ptmt) REVERT: A 547 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.7237 (ttt90) REVERT: B 38 GLU cc_start: 0.8044 (tt0) cc_final: 0.7650 (tt0) REVERT: B 170 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: B 314 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7290 (ptt90) REVERT: B 408 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7415 (ttt-90) REVERT: B 410 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: B 450 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7733 (tp) REVERT: B 467 ILE cc_start: 0.6792 (mm) cc_final: 0.6464 (mt) REVERT: B 502 GLU cc_start: 0.8004 (tt0) cc_final: 0.7737 (mp0) REVERT: B 571 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6725 (mp10) REVERT: C 1 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.5971 (mmt) REVERT: C 54 ASP cc_start: 0.7658 (t0) cc_final: 0.7211 (t0) REVERT: C 124 LYS cc_start: 0.8053 (mppt) cc_final: 0.7318 (mmmt) REVERT: C 441 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6518 (mp0) REVERT: C 546 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7271 (pt0) REVERT: C 550 ARG cc_start: 0.7666 (ttp-110) cc_final: 0.6972 (ttm-80) REVERT: D 206 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: D 269 GLU cc_start: 0.7289 (tm-30) cc_final: 0.7028 (mt-10) REVERT: D 275 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7806 (mt-10) REVERT: D 362 MET cc_start: 0.8976 (ttm) cc_final: 0.8754 (ttt) REVERT: E 7 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7822 (mm-30) REVERT: E 162 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: E 206 GLN cc_start: 0.7362 (mt0) cc_final: 0.7088 (mp10) REVERT: F 162 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: F 210 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7647 (ttm170) REVERT: F 373 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7402 (pt0) REVERT: F 391 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: G 13 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7970 (tp40) REVERT: G 38 GLU cc_start: 0.7161 (tt0) cc_final: 0.6284 (tp30) REVERT: G 137 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7101 (mt) REVERT: G 148 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6872 (mttp) REVERT: G 149 LYS cc_start: 0.7354 (mmtt) cc_final: 0.6946 (mppt) REVERT: G 160 ARG cc_start: 0.7440 (ttt90) cc_final: 0.7132 (ttt90) REVERT: H 91 ARG cc_start: 0.6441 (mmm160) cc_final: 0.5673 (mmp80) REVERT: J 148 LEU cc_start: 0.2925 (tp) cc_final: 0.2594 (pp) REVERT: J 164 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5147 (tp30) REVERT: J 172 ASP cc_start: 0.5582 (m-30) cc_final: 0.5291 (OUTLIER) REVERT: K 91 ARG cc_start: 0.4627 (ttm170) cc_final: 0.4233 (mtp85) REVERT: K 106 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6518 (mtt90) REVERT: L 119 LYS cc_start: 0.7235 (pttt) cc_final: 0.6960 (pttp) outliers start: 66 outliers final: 24 residues processed: 323 average time/residue: 1.8414 time to fit residues: 675.7888 Evaluate side-chains 300 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 259 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 227 optimal weight: 0.4980 chunk 340 optimal weight: 9.9990 chunk 360 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 322 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN B 477 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 30074 Z= 0.386 Angle : 0.618 9.192 40754 Z= 0.317 Chirality : 0.047 0.176 4567 Planarity : 0.006 0.049 5336 Dihedral : 6.808 159.155 4230 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.08 % Allowed : 11.84 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3761 helix: 0.73 (0.13), residues: 1544 sheet: 0.03 (0.21), residues: 593 loop : -0.05 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 97 HIS 0.005 0.001 HIS A 185 PHE 0.016 0.002 PHE A 230 TYR 0.016 0.002 TYR B 304 ARG 0.008 0.001 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 274 time to evaluate : 3.575 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8225 (ptpp) cc_final: 0.7697 (mttp) REVERT: A 143 PHE cc_start: 0.8621 (m-80) cc_final: 0.8297 (m-10) REVERT: A 154 ARG cc_start: 0.7647 (ptm160) cc_final: 0.7035 (ptt90) REVERT: A 197 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.7298 (ttp80) REVERT: A 323 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7305 (mtt) REVERT: A 342 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: A 441 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6864 (tt0) REVERT: A 502 GLU cc_start: 0.7808 (pm20) cc_final: 0.7419 (mp0) REVERT: A 547 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.6897 (ttm110) REVERT: B 38 GLU cc_start: 0.8003 (tt0) cc_final: 0.7602 (tt0) REVERT: B 133 MET cc_start: 0.7852 (mtt) cc_final: 0.7492 (mtp) REVERT: B 170 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: B 314 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7296 (ptt90) REVERT: B 408 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7397 (ttt-90) REVERT: B 450 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7747 (tp) REVERT: B 467 ILE cc_start: 0.6918 (mm) cc_final: 0.6542 (mt) REVERT: B 502 GLU cc_start: 0.8084 (tt0) cc_final: 0.7744 (mp0) REVERT: B 557 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: B 567 MET cc_start: 0.7536 (tpt) cc_final: 0.7192 (tpt) REVERT: C 124 LYS cc_start: 0.8084 (mppt) cc_final: 0.7343 (mmmt) REVERT: C 441 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: C 546 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7288 (pt0) REVERT: C 550 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7056 (ttm-80) REVERT: D 206 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7026 (mp10) REVERT: D 269 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7029 (mt-10) REVERT: D 275 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7809 (mt-10) REVERT: D 362 MET cc_start: 0.9010 (ttm) cc_final: 0.8775 (ttt) REVERT: D 413 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: E 7 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7924 (mm-30) REVERT: E 162 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: E 206 GLN cc_start: 0.7385 (mt0) cc_final: 0.7106 (mp10) REVERT: E 334 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7594 (mm-30) REVERT: E 470 ILE cc_start: 0.5372 (OUTLIER) cc_final: 0.5067 (mp) REVERT: F 162 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: F 275 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: F 373 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: F 391 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: G 38 GLU cc_start: 0.7029 (tt0) cc_final: 0.6210 (tp30) REVERT: G 137 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7035 (mt) REVERT: G 148 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6919 (mttp) REVERT: G 149 LYS cc_start: 0.7394 (mmtt) cc_final: 0.6955 (mppt) REVERT: G 160 ARG cc_start: 0.7405 (ttt90) cc_final: 0.7198 (ttt90) REVERT: H 91 ARG cc_start: 0.6460 (mmm160) cc_final: 0.5704 (mmp80) REVERT: J 148 LEU cc_start: 0.2747 (OUTLIER) cc_final: 0.2381 (pp) REVERT: J 164 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.4990 (tp30) REVERT: J 172 ASP cc_start: 0.5647 (m-30) cc_final: 0.5337 (OUTLIER) REVERT: K 88 TYR cc_start: 0.5734 (m-80) cc_final: 0.5498 (m-80) REVERT: K 91 ARG cc_start: 0.4676 (ttm170) cc_final: 0.4270 (mtp85) REVERT: K 106 ARG cc_start: 0.7201 (mtm-85) cc_final: 0.6748 (mtm-85) outliers start: 95 outliers final: 37 residues processed: 351 average time/residue: 1.7200 time to fit residues: 690.5443 Evaluate side-chains 313 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 256 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 0.0370 chunk 204 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 307 optimal weight: 4.9990 chunk 249 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30074 Z= 0.271 Angle : 0.554 9.000 40754 Z= 0.284 Chirality : 0.045 0.163 4567 Planarity : 0.005 0.047 5336 Dihedral : 6.625 156.927 4230 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.82 % Allowed : 13.11 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3761 helix: 0.89 (0.14), residues: 1543 sheet: 0.08 (0.21), residues: 574 loop : -0.05 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 97 HIS 0.004 0.001 HIS A 185 PHE 0.016 0.001 PHE A 230 TYR 0.012 0.001 TYR G 133 ARG 0.009 0.000 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 273 time to evaluate : 3.142 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8184 (ptpp) cc_final: 0.7728 (mttp) REVERT: A 143 PHE cc_start: 0.8591 (m-80) cc_final: 0.8274 (m-10) REVERT: A 154 ARG cc_start: 0.7612 (ptm160) cc_final: 0.6978 (ptt90) REVERT: A 197 ARG cc_start: 0.7520 (ttp-110) cc_final: 0.7243 (ttp80) REVERT: A 323 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7240 (mtt) REVERT: A 342 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: A 441 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6864 (tt0) REVERT: A 502 GLU cc_start: 0.7810 (pm20) cc_final: 0.7473 (mp0) REVERT: A 547 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7171 (ttt90) REVERT: B 38 GLU cc_start: 0.7950 (tt0) cc_final: 0.7552 (tt0) REVERT: B 133 MET cc_start: 0.7818 (mtt) cc_final: 0.7500 (mtp) REVERT: B 170 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: B 314 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7180 (ptt90) REVERT: B 408 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7381 (ttt-90) REVERT: B 450 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7684 (tp) REVERT: B 467 ILE cc_start: 0.6940 (mm) cc_final: 0.6569 (mt) REVERT: B 502 GLU cc_start: 0.8079 (tt0) cc_final: 0.7747 (mp0) REVERT: C 54 ASP cc_start: 0.7640 (t0) cc_final: 0.7219 (t0) REVERT: C 124 LYS cc_start: 0.8066 (mppt) cc_final: 0.7312 (mmmt) REVERT: C 441 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: C 461 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: C 546 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7287 (pt0) REVERT: C 550 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7033 (ttm-80) REVERT: C 567 MET cc_start: 0.8169 (mmp) cc_final: 0.7941 (mmp) REVERT: D 25 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8214 (ptmm) REVERT: D 43 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7468 (ptt180) REVERT: D 269 GLU cc_start: 0.7319 (tm-30) cc_final: 0.7047 (mt-10) REVERT: D 275 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7736 (mt-10) REVERT: D 362 MET cc_start: 0.8980 (ttm) cc_final: 0.8746 (ttt) REVERT: D 413 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7695 (mp10) REVERT: E 7 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7853 (mm-30) REVERT: E 162 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7152 (mt-10) REVERT: E 206 GLN cc_start: 0.7413 (mt0) cc_final: 0.7178 (mp10) REVERT: E 470 ILE cc_start: 0.5255 (OUTLIER) cc_final: 0.4986 (mp) REVERT: F 162 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: F 275 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: F 391 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: G 38 GLU cc_start: 0.7019 (tt0) cc_final: 0.6208 (tp30) REVERT: G 137 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7084 (mt) REVERT: G 148 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6918 (mttp) REVERT: G 149 LYS cc_start: 0.7431 (mmtt) cc_final: 0.7004 (mppt) REVERT: H 91 ARG cc_start: 0.6399 (mmm160) cc_final: 0.5692 (mmp80) REVERT: J 148 LEU cc_start: 0.2835 (tp) cc_final: 0.2469 (pp) REVERT: J 164 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.4993 (tp30) REVERT: J 172 ASP cc_start: 0.5614 (m-30) cc_final: 0.5266 (OUTLIER) REVERT: K 88 TYR cc_start: 0.5747 (m-80) cc_final: 0.5511 (m-80) REVERT: K 91 ARG cc_start: 0.4626 (ttm170) cc_final: 0.4206 (mtp85) REVERT: K 106 ARG cc_start: 0.7279 (mtm-85) cc_final: 0.6721 (mtm-85) outliers start: 87 outliers final: 38 residues processed: 341 average time/residue: 1.7173 time to fit residues: 672.0748 Evaluate side-chains 316 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 260 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 360 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 chunk 189 optimal weight: 0.3980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30074 Z= 0.202 Angle : 0.513 9.839 40754 Z= 0.261 Chirality : 0.043 0.156 4567 Planarity : 0.005 0.049 5336 Dihedral : 6.427 155.261 4230 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.73 % Allowed : 13.72 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3761 helix: 1.08 (0.14), residues: 1544 sheet: 0.14 (0.21), residues: 581 loop : 0.04 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 97 HIS 0.004 0.001 HIS L 130 PHE 0.016 0.001 PHE A 230 TYR 0.012 0.001 TYR G 133 ARG 0.010 0.000 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 282 time to evaluate : 3.660 Fit side-chains REVERT: A 124 LYS cc_start: 0.8168 (ptpp) cc_final: 0.7742 (mttp) REVERT: A 143 PHE cc_start: 0.8549 (m-80) cc_final: 0.8250 (m-10) REVERT: A 154 ARG cc_start: 0.7619 (ptm160) cc_final: 0.7006 (ptt90) REVERT: A 197 ARG cc_start: 0.7537 (ttp-110) cc_final: 0.7213 (ttp80) REVERT: A 323 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7218 (mtt) REVERT: A 342 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7097 (mt-10) REVERT: A 502 GLU cc_start: 0.7836 (pm20) cc_final: 0.7503 (mp0) REVERT: A 547 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.7162 (ttt90) REVERT: B 1 MET cc_start: 0.6320 (ttm) cc_final: 0.6110 (ttm) REVERT: B 38 GLU cc_start: 0.7924 (tt0) cc_final: 0.7509 (tt0) REVERT: B 133 MET cc_start: 0.7810 (mtt) cc_final: 0.7502 (mtp) REVERT: B 170 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: B 200 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7444 (m-30) REVERT: B 314 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7100 (ptt90) REVERT: B 408 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7377 (ttt-90) REVERT: B 467 ILE cc_start: 0.6759 (mm) cc_final: 0.6447 (mt) REVERT: B 502 GLU cc_start: 0.8082 (tt0) cc_final: 0.7666 (mp0) REVERT: B 513 TYR cc_start: 0.7806 (t80) cc_final: 0.7544 (t80) REVERT: B 567 MET cc_start: 0.7544 (tpt) cc_final: 0.7189 (tpt) REVERT: C 1 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6006 (mmt) REVERT: C 124 LYS cc_start: 0.8075 (mppt) cc_final: 0.7340 (mmmt) REVERT: C 441 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: C 461 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: C 546 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7216 (pt0) REVERT: C 550 ARG cc_start: 0.7709 (ttp-110) cc_final: 0.7017 (ttm-80) REVERT: C 570 ILE cc_start: 0.8308 (mt) cc_final: 0.7982 (mp) REVERT: D 43 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7606 (ptt180) REVERT: D 162 GLU cc_start: 0.7304 (mp0) cc_final: 0.6980 (mp0) REVERT: D 275 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 362 MET cc_start: 0.8935 (ttm) cc_final: 0.8717 (ttt) REVERT: D 413 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: E 7 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7790 (mm-30) REVERT: E 162 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7115 (mt-10) REVERT: E 206 GLN cc_start: 0.7416 (mt0) cc_final: 0.7193 (mp10) REVERT: F 275 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: F 370 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6872 (mptt) REVERT: F 391 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: G 137 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7107 (mt) REVERT: G 148 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6947 (mttp) REVERT: G 149 LYS cc_start: 0.7424 (mmtt) cc_final: 0.7000 (mppt) REVERT: H 91 ARG cc_start: 0.6361 (mmm160) cc_final: 0.5644 (mmp80) REVERT: J 148 LEU cc_start: 0.2849 (OUTLIER) cc_final: 0.1879 (mm) REVERT: J 164 GLU cc_start: 0.5829 (OUTLIER) cc_final: 0.4969 (tp30) REVERT: K 88 TYR cc_start: 0.5787 (m-80) cc_final: 0.5553 (m-80) REVERT: K 91 ARG cc_start: 0.4781 (ttm170) cc_final: 0.4359 (mtp85) REVERT: K 106 ARG cc_start: 0.7358 (mtm-85) cc_final: 0.6708 (mtm-85) REVERT: L 138 ARG cc_start: 0.6756 (mmm160) cc_final: 0.6462 (tpp-160) outliers start: 84 outliers final: 34 residues processed: 347 average time/residue: 1.6880 time to fit residues: 672.5716 Evaluate side-chains 314 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 262 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 359 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 219 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30074 Z= 0.182 Angle : 0.505 11.278 40754 Z= 0.256 Chirality : 0.043 0.159 4567 Planarity : 0.005 0.051 5336 Dihedral : 6.317 155.126 4230 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.53 % Allowed : 14.54 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3761 helix: 1.19 (0.14), residues: 1541 sheet: 0.23 (0.21), residues: 587 loop : 0.11 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 97 HIS 0.004 0.001 HIS L 130 PHE 0.015 0.001 PHE A 230 TYR 0.014 0.001 TYR H 89 ARG 0.009 0.000 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 272 time to evaluate : 3.239 Fit side-chains REVERT: A 124 LYS cc_start: 0.8151 (ptpp) cc_final: 0.7710 (mttp) REVERT: A 143 PHE cc_start: 0.8544 (m-80) cc_final: 0.8254 (m-10) REVERT: A 154 ARG cc_start: 0.7606 (ptm160) cc_final: 0.6997 (ptt90) REVERT: A 197 ARG cc_start: 0.7538 (ttp-110) cc_final: 0.7224 (ttp80) REVERT: A 323 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7196 (mtt) REVERT: A 342 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7047 (mt-10) REVERT: A 502 GLU cc_start: 0.7836 (pm20) cc_final: 0.7500 (mp0) REVERT: A 547 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.7164 (ttt90) REVERT: B 38 GLU cc_start: 0.7945 (tt0) cc_final: 0.7531 (tt0) REVERT: B 133 MET cc_start: 0.7798 (mtt) cc_final: 0.7552 (mtp) REVERT: B 170 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: B 200 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: B 314 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7063 (ptt90) REVERT: B 408 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7423 (ttt-90) REVERT: B 467 ILE cc_start: 0.6712 (mm) cc_final: 0.6401 (mt) REVERT: B 502 GLU cc_start: 0.8075 (tt0) cc_final: 0.7672 (mp0) REVERT: B 513 TYR cc_start: 0.7739 (t80) cc_final: 0.7482 (t80) REVERT: B 567 MET cc_start: 0.7517 (tpt) cc_final: 0.7214 (tpt) REVERT: C 1 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.5979 (mmt) REVERT: C 124 LYS cc_start: 0.8051 (mppt) cc_final: 0.7311 (mmmt) REVERT: C 441 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: C 461 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: C 550 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.6990 (ttm-80) REVERT: D 25 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8170 (ptmm) REVERT: D 43 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7645 (ptt180) REVERT: D 162 GLU cc_start: 0.7317 (mp0) cc_final: 0.6989 (mp0) REVERT: D 206 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7098 (mp10) REVERT: D 269 GLU cc_start: 0.7268 (tm-30) cc_final: 0.7032 (mt-10) REVERT: D 275 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7748 (mt-10) REVERT: D 362 MET cc_start: 0.8952 (ttm) cc_final: 0.8735 (ttt) REVERT: D 413 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: E 7 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7772 (mm-30) REVERT: E 206 GLN cc_start: 0.7411 (mt0) cc_final: 0.7189 (mp10) REVERT: E 470 ILE cc_start: 0.5424 (OUTLIER) cc_final: 0.4993 (mp) REVERT: F 128 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7389 (mm-30) REVERT: F 370 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6845 (mptt) REVERT: F 391 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: F 413 GLN cc_start: 0.7822 (mt0) cc_final: 0.7558 (mt0) REVERT: G 148 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6878 (mttp) REVERT: G 149 LYS cc_start: 0.7388 (mmtt) cc_final: 0.6972 (mppt) REVERT: H 91 ARG cc_start: 0.6398 (mmm160) cc_final: 0.5680 (mmp80) REVERT: J 148 LEU cc_start: 0.2809 (tp) cc_final: 0.1880 (mm) REVERT: J 164 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5035 (tp30) REVERT: J 172 ASP cc_start: 0.5500 (m-30) cc_final: 0.5119 (OUTLIER) REVERT: K 88 TYR cc_start: 0.5797 (m-80) cc_final: 0.5568 (m-80) REVERT: K 91 ARG cc_start: 0.4834 (ttm170) cc_final: 0.4395 (mtp85) REVERT: K 104 MET cc_start: 0.6471 (ttm) cc_final: 0.6208 (ttp) REVERT: K 106 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.6840 (mtm-85) REVERT: L 138 ARG cc_start: 0.6732 (mmm160) cc_final: 0.6488 (tpp-160) REVERT: L 184 GLN cc_start: 0.5843 (tt0) cc_final: 0.5613 (tm130) outliers start: 78 outliers final: 38 residues processed: 335 average time/residue: 1.6561 time to fit residues: 637.4447 Evaluate side-chains 316 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 262 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 282 optimal weight: 0.0980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN G 10 ASN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30074 Z= 0.166 Angle : 0.500 11.220 40754 Z= 0.252 Chirality : 0.042 0.161 4567 Planarity : 0.005 0.046 5336 Dihedral : 6.232 155.335 4230 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.40 % Allowed : 14.96 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3761 helix: 1.27 (0.14), residues: 1541 sheet: 0.26 (0.21), residues: 587 loop : 0.15 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 119 HIS 0.003 0.001 HIS A 185 PHE 0.015 0.001 PHE A 230 TYR 0.011 0.001 TYR G 133 ARG 0.009 0.000 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 270 time to evaluate : 3.407 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7712 (mttp) REVERT: A 143 PHE cc_start: 0.8507 (m-80) cc_final: 0.8214 (m-10) REVERT: A 154 ARG cc_start: 0.7603 (ptm160) cc_final: 0.7033 (ptt90) REVERT: A 197 ARG cc_start: 0.7540 (ttp-110) cc_final: 0.7228 (ttp80) REVERT: A 220 MET cc_start: 0.8016 (tpp) cc_final: 0.7776 (tpt) REVERT: A 323 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7199 (mtt) REVERT: A 342 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6984 (mt-10) REVERT: A 502 GLU cc_start: 0.7838 (pm20) cc_final: 0.7506 (mp0) REVERT: A 547 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7170 (ttt90) REVERT: B 38 GLU cc_start: 0.7933 (tt0) cc_final: 0.7523 (tt0) REVERT: B 133 MET cc_start: 0.7796 (mtt) cc_final: 0.7534 (mtp) REVERT: B 170 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: B 200 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: B 276 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7580 (ttmm) REVERT: B 314 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7051 (ptt90) REVERT: B 408 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7437 (ttt-90) REVERT: B 467 ILE cc_start: 0.6624 (mm) cc_final: 0.6347 (mt) REVERT: B 502 GLU cc_start: 0.8069 (tt0) cc_final: 0.7734 (mp0) REVERT: B 532 ARG cc_start: 0.6446 (OUTLIER) cc_final: 0.5690 (ttp80) REVERT: B 567 MET cc_start: 0.7525 (tpt) cc_final: 0.7226 (tpt) REVERT: C 1 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.5973 (mmt) REVERT: C 124 LYS cc_start: 0.8052 (mppt) cc_final: 0.7322 (mmmt) REVERT: C 130 ARG cc_start: 0.7278 (mtp-110) cc_final: 0.6845 (ttp-110) REVERT: C 441 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: C 461 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: C 550 ARG cc_start: 0.7689 (ttp-110) cc_final: 0.7050 (ttm-80) REVERT: D 25 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8162 (ptmm) REVERT: D 43 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7583 (ptt180) REVERT: D 162 GLU cc_start: 0.7314 (mp0) cc_final: 0.6986 (mp0) REVERT: D 206 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7097 (mp10) REVERT: D 269 GLU cc_start: 0.7264 (tm-30) cc_final: 0.7028 (mt-10) REVERT: D 275 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7747 (mt-10) REVERT: D 362 MET cc_start: 0.8947 (ttm) cc_final: 0.8738 (ttt) REVERT: D 413 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: E 7 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7751 (mm-30) REVERT: E 206 GLN cc_start: 0.7367 (mt0) cc_final: 0.7144 (mp10) REVERT: E 470 ILE cc_start: 0.5422 (OUTLIER) cc_final: 0.5009 (mp) REVERT: F 128 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7382 (mm-30) REVERT: F 413 GLN cc_start: 0.7906 (mt0) cc_final: 0.7634 (mt0) REVERT: G 137 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6941 (mt) REVERT: G 148 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6809 (mttp) REVERT: G 149 LYS cc_start: 0.7390 (mmtt) cc_final: 0.6981 (mppt) REVERT: H 91 ARG cc_start: 0.6360 (mmm160) cc_final: 0.5668 (mmp80) REVERT: J 148 LEU cc_start: 0.2809 (tp) cc_final: 0.1884 (mm) REVERT: J 164 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5033 (tp30) REVERT: J 172 ASP cc_start: 0.5632 (m-30) cc_final: 0.5191 (m-30) REVERT: K 91 ARG cc_start: 0.4964 (ttm170) cc_final: 0.4759 (ttp80) REVERT: K 104 MET cc_start: 0.6485 (ttm) cc_final: 0.6230 (ttp) REVERT: K 106 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.6824 (mtm-85) outliers start: 74 outliers final: 39 residues processed: 331 average time/residue: 1.6986 time to fit residues: 648.8152 Evaluate side-chains 319 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 262 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 0.7980 chunk 344 optimal weight: 20.0000 chunk 314 optimal weight: 8.9990 chunk 335 optimal weight: 30.0000 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 316 optimal weight: 20.0000 chunk 333 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 541 GLN A 571 GLN F 23 ASN G 13 GLN G 180 GLN ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 30074 Z= 0.382 Angle : 0.608 13.897 40754 Z= 0.309 Chirality : 0.047 0.171 4567 Planarity : 0.005 0.057 5336 Dihedral : 6.613 154.586 4230 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.66 % Allowed : 14.93 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3761 helix: 0.90 (0.14), residues: 1551 sheet: 0.07 (0.21), residues: 607 loop : -0.04 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 97 HIS 0.006 0.001 HIS L 130 PHE 0.017 0.002 PHE H 13 TYR 0.015 0.002 TYR C 428 ARG 0.009 0.001 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 259 time to evaluate : 3.455 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8170 (ptpp) cc_final: 0.7733 (mttp) REVERT: A 143 PHE cc_start: 0.8581 (m-80) cc_final: 0.8328 (m-10) REVERT: A 154 ARG cc_start: 0.7565 (ptm160) cc_final: 0.6992 (ptt90) REVERT: A 197 ARG cc_start: 0.7534 (ttp-110) cc_final: 0.7262 (ttp80) REVERT: A 220 MET cc_start: 0.8049 (tpp) cc_final: 0.7798 (tpt) REVERT: A 323 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7332 (mtt) REVERT: A 342 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: A 441 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6896 (tt0) REVERT: A 502 GLU cc_start: 0.7798 (pm20) cc_final: 0.7484 (mp0) REVERT: A 547 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.7169 (ttt90) REVERT: B 38 GLU cc_start: 0.8001 (tt0) cc_final: 0.7583 (tt0) REVERT: B 133 MET cc_start: 0.7825 (mtt) cc_final: 0.7560 (mtp) REVERT: B 170 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7302 (tp30) REVERT: B 276 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7591 (ttmm) REVERT: B 314 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7252 (ptt90) REVERT: B 408 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7380 (ttt-90) REVERT: B 467 ILE cc_start: 0.6713 (mm) cc_final: 0.6336 (mt) REVERT: B 502 GLU cc_start: 0.8097 (tt0) cc_final: 0.7735 (mp0) REVERT: B 567 MET cc_start: 0.7465 (tpt) cc_final: 0.7186 (tpt) REVERT: C 124 LYS cc_start: 0.8138 (mppt) cc_final: 0.7370 (mmmt) REVERT: C 441 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: C 461 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: C 550 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7125 (ttm-80) REVERT: D 25 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8212 (ptmm) REVERT: D 43 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7729 (ptt180) REVERT: D 206 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: D 269 GLU cc_start: 0.7303 (tm-30) cc_final: 0.7042 (mt-10) REVERT: D 275 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7796 (mt-10) REVERT: D 362 MET cc_start: 0.9005 (ttm) cc_final: 0.8708 (ttt) REVERT: D 413 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7678 (mp10) REVERT: E 7 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7782 (mm-30) REVERT: E 206 GLN cc_start: 0.7408 (mt0) cc_final: 0.7119 (mp10) REVERT: E 442 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7785 (mt) REVERT: E 470 ILE cc_start: 0.5381 (OUTLIER) cc_final: 0.4953 (mp) REVERT: G 148 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6863 (mttp) REVERT: G 149 LYS cc_start: 0.7401 (mmtt) cc_final: 0.6974 (mppt) REVERT: H 91 ARG cc_start: 0.6390 (mmm160) cc_final: 0.5657 (mmp80) REVERT: J 164 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.4886 (tp30) REVERT: J 172 ASP cc_start: 0.5654 (m-30) cc_final: 0.5208 (m-30) REVERT: K 91 ARG cc_start: 0.4669 (ttm170) cc_final: 0.4231 (mtp85) REVERT: K 104 MET cc_start: 0.6486 (ttm) cc_final: 0.6242 (ttp) REVERT: K 106 ARG cc_start: 0.7401 (mtm-85) cc_final: 0.6775 (mtm-85) outliers start: 82 outliers final: 46 residues processed: 326 average time/residue: 1.8258 time to fit residues: 695.1240 Evaluate side-chains 315 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 253 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.8980 chunk 354 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 246 optimal weight: 0.7980 chunk 371 optimal weight: 5.9990 chunk 342 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 228 optimal weight: 0.4980 chunk 181 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 541 GLN ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30074 Z= 0.168 Angle : 0.501 8.544 40754 Z= 0.255 Chirality : 0.042 0.162 4567 Planarity : 0.005 0.045 5336 Dihedral : 6.298 153.365 4230 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.04 % Allowed : 15.74 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3761 helix: 1.21 (0.14), residues: 1540 sheet: 0.19 (0.22), residues: 555 loop : 0.07 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 97 HIS 0.004 0.001 HIS L 130 PHE 0.015 0.001 PHE A 230 TYR 0.017 0.001 TYR B 513 ARG 0.009 0.000 ARG D 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 259 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8140 (ptpp) cc_final: 0.7743 (mttp) REVERT: A 154 ARG cc_start: 0.7574 (ptm160) cc_final: 0.6987 (ptt90) REVERT: A 197 ARG cc_start: 0.7520 (ttp-110) cc_final: 0.7204 (ttp80) REVERT: A 323 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7224 (mtt) REVERT: A 342 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7092 (mt-10) REVERT: A 425 ASN cc_start: 0.8677 (t0) cc_final: 0.8409 (t0) REVERT: A 502 GLU cc_start: 0.7745 (pm20) cc_final: 0.7415 (mp0) REVERT: A 547 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7149 (ttt90) REVERT: B 38 GLU cc_start: 0.7927 (tt0) cc_final: 0.7505 (tt0) REVERT: B 133 MET cc_start: 0.7781 (mtt) cc_final: 0.7529 (mtp) REVERT: B 170 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7297 (tp30) REVERT: B 314 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7072 (ptt90) REVERT: B 408 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7418 (ttt-90) REVERT: B 467 ILE cc_start: 0.6678 (mm) cc_final: 0.6352 (mt) REVERT: B 502 GLU cc_start: 0.8078 (tt0) cc_final: 0.7734 (mp0) REVERT: B 567 MET cc_start: 0.7552 (tpt) cc_final: 0.7264 (tpt) REVERT: C 124 LYS cc_start: 0.8081 (mppt) cc_final: 0.7299 (mmmt) REVERT: C 130 ARG cc_start: 0.7309 (mtp-110) cc_final: 0.6912 (ttp-110) REVERT: C 441 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: C 550 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7089 (ttm-80) REVERT: D 25 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8147 (ptmm) REVERT: D 43 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7664 (ptt180) REVERT: D 206 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7072 (mp10) REVERT: D 269 GLU cc_start: 0.7280 (tm-30) cc_final: 0.7050 (mt-10) REVERT: D 275 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7741 (mt-10) REVERT: D 362 MET cc_start: 0.8943 (ttm) cc_final: 0.8731 (ttt) REVERT: D 413 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: E 7 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7911 (mm-30) REVERT: E 206 GLN cc_start: 0.7385 (mt0) cc_final: 0.7163 (mp10) REVERT: E 470 ILE cc_start: 0.5453 (OUTLIER) cc_final: 0.5056 (mp) REVERT: F 128 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7405 (mm-30) REVERT: F 413 GLN cc_start: 0.7858 (mt0) cc_final: 0.7560 (mt0) REVERT: G 148 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6921 (mttp) REVERT: G 149 LYS cc_start: 0.7390 (mmtt) cc_final: 0.6971 (mppt) REVERT: H 91 ARG cc_start: 0.6428 (mmm160) cc_final: 0.5705 (mmp80) REVERT: J 148 LEU cc_start: 0.2719 (OUTLIER) cc_final: 0.1817 (mm) REVERT: J 164 GLU cc_start: 0.5836 (OUTLIER) cc_final: 0.4992 (tp30) REVERT: J 172 ASP cc_start: 0.5589 (m-30) cc_final: 0.5176 (m-30) REVERT: K 91 ARG cc_start: 0.4694 (ttm170) cc_final: 0.4220 (mtp85) REVERT: K 104 MET cc_start: 0.6447 (ttm) cc_final: 0.6195 (ttp) REVERT: K 106 ARG cc_start: 0.7393 (mtm-85) cc_final: 0.6801 (mtm-85) REVERT: L 184 GLN cc_start: 0.5842 (tm-30) cc_final: 0.5605 (tm130) outliers start: 63 outliers final: 40 residues processed: 313 average time/residue: 1.7630 time to fit residues: 631.6000 Evaluate side-chains 310 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 257 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 5.9990 chunk 315 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 296 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN G 13 GLN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.087030 restraints weight = 44434.336| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.68 r_work: 0.2943 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30074 Z= 0.263 Angle : 0.542 9.281 40754 Z= 0.275 Chirality : 0.044 0.159 4567 Planarity : 0.005 0.052 5336 Dihedral : 6.415 152.839 4230 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.34 % Allowed : 15.41 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3761 helix: 1.08 (0.14), residues: 1550 sheet: 0.11 (0.21), residues: 587 loop : 0.02 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 97 HIS 0.004 0.001 HIS A 185 PHE 0.015 0.001 PHE A 230 TYR 0.016 0.001 TYR B 513 ARG 0.009 0.000 ARG D 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11137.20 seconds wall clock time: 198 minutes 2.33 seconds (11882.33 seconds total)