Starting phenix.real_space_refine on Wed Feb 21 03:46:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vam_31850/02_2024/7vam_31850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vam_31850/02_2024/7vam_31850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vam_31850/02_2024/7vam_31850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vam_31850/02_2024/7vam_31850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vam_31850/02_2024/7vam_31850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vam_31850/02_2024/7vam_31850_updated.pdb" } resolution = 3.2 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= 0.006 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 9 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 363": "OE1" <-> "OE2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29558 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} 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: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} 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: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 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: 15.75, per 1000 atoms: 0.53 Number of scatterers: 29558 At special positions: 0 Unit cell: (149.6, 147.84, 177.76, 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 9 15.00 Mg 2 11.99 O 5578 8.00 N 5131 7.00 C 18735 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: 11.98 Conformation dependent library (CDL) restraints added in 5.5 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 135 helices and 37 sheets defined 41.9% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.60 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 243 Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.876A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) 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: 4.448A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.755A pdb=" N ALA A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.233A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.732A 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 432 through 442 Proline residue: A 437 - end of helix removed outlier: 3.544A pdb=" N GLU A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.912A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (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 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.845A pdb=" N ARG A 550 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 577 Proline residue: A 560 - end of helix removed outlier: 3.890A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (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: 4.664A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.814A 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: 3.924A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 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 471 removed outlier: 3.781A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (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: 3.963A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.616A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (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 243 Processing helix chain 'C' and resid 259 through 271 removed outlier: 3.811A 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: 3.571A 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: 3.901A 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: 3.604A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 433 through 442 Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 447 through 471 removed outlier: 3.954A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) 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 541 Processing helix chain 'C' and resid 544 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 573 Proline residue: C 560 - end of helix Processing helix chain 'C' and resid 575 through 577 No H-bonds generated for 'chain 'C' and resid 575 through 577' 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 141 removed outlier: 3.561A pdb=" N MET D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 198 through 211 removed outlier: 3.942A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) 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: 3.504A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.936A 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 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.866A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE D 392 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 403 No H-bonds generated for 'chain 'D' and resid 401 through 403' Processing helix chain 'D' and resid 406 through 421 removed outlier: 3.514A pdb=" N ARG D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.817A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 468 through 471 No H-bonds generated for 'chain 'D' and resid 468 through 471' 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 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 214 through 216 No H-bonds generated for 'chain 'E' and resid 214 through 216' Processing helix chain 'E' and resid 229 through 249 removed outlier: 3.887A pdb=" N THR E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.545A pdb=" N PHE E 247 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 248 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N HIS E 249 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.604A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG E 297 " --> pdb=" O THR E 293 " (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 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 375 through 399 removed outlier: 4.136A 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 445 removed outlier: 4.010A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) 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 456 through 462 Processing helix chain 'E' and resid 467 through 469 No H-bonds generated for 'chain 'E' and resid 467 through 469' Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' 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 228 through 249 removed outlier: 3.840A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.589A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.130A 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 285 through 295 removed outlier: 4.255A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR F 295 " --> pdb=" O ALA F 292 " (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 345 Processing helix chain 'F' and resid 362 through 365 No H-bonds generated for 'chain 'F' and resid 362 through 365' Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.765A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (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: 3.823A 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 68 removed outlier: 3.741A pdb=" N GLU G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 206 removed outlier: 4.566A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 5.328A 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 14 removed outlier: 3.925A pdb=" N GLN H 11 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE H 13 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.811A pdb=" N LYS I 97 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.562A pdb=" N GLU I 117 " --> pdb=" O LEU I 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 93 removed outlier: 3.757A pdb=" N ALA J 93 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 114 removed outlier: 3.936A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 Proline residue: J 129 - end of helix removed outlier: 4.717A pdb=" N GLU J 132 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA J 135 " --> pdb=" O GLU J 132 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 167 through 186 removed outlier: 5.480A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.790A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'L' and resid 62 through 92 removed outlier: 3.691A pdb=" N LEU L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL L 68 " --> pdb=" O GLY L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix removed outlier: 3.810A pdb=" N VAL L 104 " --> pdb=" O PRO L 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG L 105 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 4.466A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 3.677A pdb=" N ASP L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.626A 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: 6.576A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.600A 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 76 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.007A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 384 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.738A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 137 through 140 Processing sheet with id= F, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.726A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.895A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.631A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.691A 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 75 Processing sheet with id= J, first strand: chain 'B' and resid 117 through 119 Processing sheet with id= K, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= L, first strand: chain 'B' and resid 197 through 199 removed outlier: 3.671A pdb=" N ARG B 197 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS B 367 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 380 through 384 removed outlier: 6.881A pdb=" N ALA B 405 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N TRP B 407 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.667A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.659A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 63 through 66 removed outlier: 3.969A pdb=" N ILE C 2 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE C 15 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE C 9 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU C 69 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS C 29 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR C 67 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= R, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.128A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 164 through 166 removed outlier: 5.639A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 197 through 199 removed outlier: 3.556A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS C 367 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.975A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 7 through 9 removed outlier: 6.710A pdb=" N ILE D 32 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR D 13 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU D 22 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE D 11 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.644A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Y, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.560A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 77 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= AA, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AB, first strand: chain 'E' and resid 307 through 312 removed outlier: 3.686A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA E 188 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE E 256 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.580A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.477A 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 Processing sheet with id= AE, first strand: chain 'F' and resid 92 through 94 removed outlier: 8.079A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.758A 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 94 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 120 through 123 removed outlier: 6.576A pdb=" N GLU J 141 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ALA J 123 " --> pdb=" O GLU J 141 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN J 143 " --> pdb=" O ALA J 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'J' and resid 153 through 155 Processing sheet with id= AK, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.963A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) 1214 hydrogen bonds defined for protein. 3297 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: 9.89 Time building geometry restraints manager: 12.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9948 1.34 - 1.46: 3814 1.46 - 1.57: 16145 1.57 - 1.69: 13 1.69 - 1.80: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.36e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.33e+01 bond pdb=" C5 ATP C 601 " pdb=" C6 ATP C 601 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.58e+01 bond pdb=" C5 ATP C 601 " pdb=" N7 ATP C 601 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.46e+01 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.83: 1049 106.83 - 114.18: 17270 114.18 - 121.54: 15797 121.54 - 128.90: 6547 128.90 - 136.26: 150 Bond angle restraints: 40813 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 121.35 18.52 1.00e+00 1.00e+00 3.43e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 121.58 18.29 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 120.29 16.54 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 122.06 14.77 1.00e+00 1.00e+00 2.18e+02 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 118.38 8.42 1.00e+00 1.00e+00 7.08e+01 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 17538 24.83 - 49.65: 722 49.65 - 74.48: 92 74.48 - 99.31: 30 99.31 - 124.13: 1 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: 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 300.00 175.86 124.13 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 32.58 -92.58 1 2.00e+01 2.50e-03 2.51e+01 dihedral pdb=" CA ARG A 23 " pdb=" C ARG A 23 " pdb=" N MET A 24 " pdb=" CA MET A 24 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 4571 0.287 - 0.574: 0 0.574 - 0.861: 0 0.861 - 1.148: 0 1.148 - 1.436: 1 Chirality restraints: 4572 Sorted by residual: chirality pdb=" C4' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" C5' ATP B 601 " pdb=" O4' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.49 -1.06 -1.44 2.00e-01 2.50e+01 5.15e+01 chirality pdb=" CB ILE B 211 " pdb=" CA ILE B 211 " pdb=" CG1 ILE B 211 " pdb=" CG2 ILE B 211 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.51 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 101 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO G 102 " -0.078 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 ILE B 226 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 227 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO E 324 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.021 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 12 2.29 - 2.94: 12609 2.94 - 3.59: 42411 3.59 - 4.25: 67585 4.25 - 4.90: 116812 Nonbonded interactions: 239429 Sorted by model distance: nonbonded pdb=" OG SER A 235 " pdb="MG MG A 602 " model vdw 1.634 2.170 nonbonded pdb=" O LEU B 241 " pdb=" OG SER B 245 " model vdw 2.146 2.440 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.147 2.440 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.160 2.440 nonbonded pdb=" OG1 THR C 167 " pdb=" OE1 GLU C 170 " model vdw 2.163 2.440 ... (remaining 239424 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 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.940 Check model and map are aligned: 0.450 Set scattering table: 0.260 Process input model: 78.120 Find NCS groups from input model: 1.840 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 0.073 30114 Z= 0.228 Angle : 0.608 18.521 40813 Z= 0.377 Chirality : 0.048 1.436 4572 Planarity : 0.004 0.045 5333 Dihedral : 13.552 124.132 11465 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 1.25 (0.14), residues: 3764 helix: 1.70 (0.14), residues: 1560 sheet: 0.14 (0.21), residues: 643 loop : 0.39 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 100 HIS 0.002 0.001 HIS L 130 PHE 0.012 0.001 PHE C 406 TYR 0.014 0.001 TYR E 13 ARG 0.007 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 3.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8088 (ptmm) cc_final: 0.7748 (pttp) REVERT: A 24 MET cc_start: 0.7983 (tpt) cc_final: 0.7606 (tpt) REVERT: A 74 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8085 (mt-10) REVERT: A 124 LYS cc_start: 0.7217 (mptt) cc_final: 0.6892 (mmtm) REVERT: A 300 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7073 (tp30) REVERT: A 329 ARG cc_start: 0.4982 (mtm-85) cc_final: 0.4427 (mmp80) REVERT: A 330 TRP cc_start: 0.7857 (t60) cc_final: 0.7626 (t60) REVERT: A 347 GLU cc_start: 0.6473 (tt0) cc_final: 0.5854 (pm20) REVERT: A 456 GLU cc_start: 0.7314 (tt0) cc_final: 0.6659 (mt-10) REVERT: A 469 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6967 (mt0) REVERT: A 527 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6940 (mm-30) REVERT: A 550 ARG cc_start: 0.7181 (mmt180) cc_final: 0.6955 (mmm160) REVERT: A 569 GLU cc_start: 0.5446 (tt0) cc_final: 0.4991 (mm-30) REVERT: B 124 LYS cc_start: 0.5667 (mmtm) cc_final: 0.5374 (mtpp) REVERT: B 133 MET cc_start: 0.7708 (mtp) cc_final: 0.7445 (mtm) REVERT: B 172 VAL cc_start: 0.8319 (t) cc_final: 0.7947 (m) REVERT: B 197 ARG cc_start: 0.7760 (ttp-110) cc_final: 0.7396 (ttp-110) REVERT: B 257 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7048 (mm-30) REVERT: B 363 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6938 (mm-30) REVERT: B 441 GLU cc_start: 0.6392 (tp30) cc_final: 0.6164 (tt0) REVERT: B 474 ASP cc_start: 0.6454 (t0) cc_final: 0.5981 (p0) REVERT: B 485 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6899 (mm-30) REVERT: B 489 ILE cc_start: 0.6341 (mt) cc_final: 0.6128 (mt) REVERT: B 506 TYR cc_start: 0.7182 (t80) cc_final: 0.6892 (t80) REVERT: B 520 LEU cc_start: 0.7320 (mm) cc_final: 0.7025 (mm) REVERT: B 524 LYS cc_start: 0.5185 (mtmt) cc_final: 0.4759 (tttm) REVERT: C 124 LYS cc_start: 0.7360 (ptpp) cc_final: 0.6380 (mttm) REVERT: C 130 ARG cc_start: 0.7313 (mtm180) cc_final: 0.7102 (mtp85) REVERT: C 156 ARG cc_start: 0.7540 (ttp-170) cc_final: 0.7213 (ttt-90) REVERT: C 160 VAL cc_start: 0.8777 (t) cc_final: 0.8507 (m) REVERT: C 220 MET cc_start: 0.7736 (mmt) cc_final: 0.7402 (tpt) REVERT: C 441 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6573 (tt0) REVERT: C 481 ARG cc_start: 0.6402 (mtp85) cc_final: 0.6123 (ttt-90) REVERT: C 527 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6826 (pp20) REVERT: C 568 LYS cc_start: 0.7071 (mmtm) cc_final: 0.6861 (mttm) REVERT: D 15 SER cc_start: 0.7997 (t) cc_final: 0.7693 (p) REVERT: D 234 THR cc_start: 0.7241 (m) cc_final: 0.7028 (m) REVERT: D 275 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7537 (mt-10) REVERT: E 210 ARG cc_start: 0.7770 (ttp80) cc_final: 0.7119 (ttt-90) REVERT: E 265 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6738 (mt-10) REVERT: E 290 ASP cc_start: 0.7315 (t70) cc_final: 0.6937 (t0) REVERT: E 334 GLU cc_start: 0.8569 (mp0) cc_final: 0.8272 (mp0) REVERT: F 3 LEU cc_start: 0.6536 (mp) cc_final: 0.6213 (mp) REVERT: F 6 LYS cc_start: 0.7578 (tttt) cc_final: 0.6235 (ptpp) REVERT: F 13 TYR cc_start: 0.8991 (t80) cc_final: 0.8758 (t80) REVERT: F 223 LYS cc_start: 0.6999 (mttp) cc_final: 0.6250 (mppt) REVERT: F 280 ARG cc_start: 0.7419 (ttp-170) cc_final: 0.7207 (ttp-170) REVERT: F 318 ASP cc_start: 0.7522 (p0) cc_final: 0.6697 (t0) REVERT: F 363 ASN cc_start: 0.8093 (m-40) cc_final: 0.7565 (t0) REVERT: F 413 GLN cc_start: 0.7264 (mt0) cc_final: 0.7014 (mt0) REVERT: F 420 ARG cc_start: 0.6894 (mtm110) cc_final: 0.6635 (mtm-85) REVERT: G 15 ARG cc_start: 0.6606 (mtt180) cc_final: 0.6390 (mtp85) REVERT: G 17 GLN cc_start: 0.6945 (mm-40) cc_final: 0.6639 (mm110) REVERT: G 19 ARG cc_start: 0.6685 (ttm110) cc_final: 0.6349 (ttm110) REVERT: G 47 MET cc_start: 0.5410 (ppp) cc_final: 0.5189 (tpp) REVERT: G 148 LYS cc_start: 0.5872 (mtpt) cc_final: 0.5628 (mttm) REVERT: G 177 ARG cc_start: 0.6836 (ttm110) cc_final: 0.6211 (ttt-90) REVERT: G 187 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6698 (mm-30) REVERT: H 1 MET cc_start: 0.3170 (mpp) cc_final: 0.2799 (mtm) REVERT: J 81 GLU cc_start: 0.5453 (pp20) cc_final: 0.4820 (tt0) REVERT: J 88 ARG cc_start: 0.5285 (ptm160) cc_final: 0.4622 (ttp-170) REVERT: J 89 GLU cc_start: 0.5176 (tp30) cc_final: 0.4890 (mm-30) REVERT: J 115 LEU cc_start: 0.5101 (tt) cc_final: 0.4869 (tp) REVERT: K 104 MET cc_start: 0.6393 (mtp) cc_final: 0.5851 (tpt) REVERT: L 81 GLU cc_start: 0.6912 (tt0) cc_final: 0.6449 (mt-10) REVERT: L 110 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6808 (tt0) REVERT: L 142 LEU cc_start: 0.6559 (pt) cc_final: 0.5913 (mt) REVERT: L 160 LYS cc_start: 0.6321 (mmtp) cc_final: 0.5659 (mmpt) REVERT: L 168 LEU cc_start: 0.6808 (pp) cc_final: 0.6430 (tt) REVERT: L 172 ASP cc_start: 0.7550 (t70) cc_final: 0.7112 (m-30) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.5097 time to fit residues: 414.2402 Evaluate side-chains 342 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 151 optimal weight: 0.4980 chunk 292 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 338 optimal weight: 2.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 397 GLN D 170 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 437 GLN E 142 ASN E 338 GLN F 425 GLN F 465 GLN H 82 GLN L 74 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30114 Z= 0.270 Angle : 0.558 8.372 40813 Z= 0.289 Chirality : 0.045 0.156 4572 Planarity : 0.005 0.046 5333 Dihedral : 6.483 116.114 4259 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.94 % Allowed : 6.68 % Favored : 92.38 % 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: 0.96 (0.14), residues: 3764 helix: 1.37 (0.14), residues: 1556 sheet: 0.38 (0.22), residues: 579 loop : 0.14 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 119 HIS 0.005 0.001 HIS A 185 PHE 0.024 0.002 PHE A 230 TYR 0.020 0.002 TYR E 13 ARG 0.007 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 327 time to evaluate : 3.521 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7963 (ptmm) cc_final: 0.7615 (pttp) REVERT: A 24 MET cc_start: 0.7954 (tpt) cc_final: 0.7592 (tpt) REVERT: A 74 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8129 (mt-10) REVERT: A 124 LYS cc_start: 0.7176 (mptt) cc_final: 0.6860 (mmtm) REVERT: A 329 ARG cc_start: 0.5501 (mtm-85) cc_final: 0.4785 (mmp80) REVERT: A 347 GLU cc_start: 0.6433 (tt0) cc_final: 0.5667 (pm20) REVERT: A 353 TYR cc_start: 0.7960 (p90) cc_final: 0.7703 (p90) REVERT: A 456 GLU cc_start: 0.7432 (tt0) cc_final: 0.6764 (mt-10) REVERT: A 469 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6884 (mt0) REVERT: A 527 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6957 (mm-30) REVERT: A 569 GLU cc_start: 0.5639 (tt0) cc_final: 0.5023 (mm-30) REVERT: B 124 LYS cc_start: 0.5856 (mmtm) cc_final: 0.5379 (mtpp) REVERT: B 197 ARG cc_start: 0.7810 (ttp-110) cc_final: 0.7343 (ttp-110) REVERT: B 441 GLU cc_start: 0.6377 (tp30) cc_final: 0.6158 (tt0) REVERT: B 474 ASP cc_start: 0.6417 (t0) cc_final: 0.5947 (p0) REVERT: B 509 MET cc_start: 0.6549 (mmt) cc_final: 0.6338 (mmt) REVERT: B 520 LEU cc_start: 0.7333 (mm) cc_final: 0.6989 (mm) REVERT: B 524 LYS cc_start: 0.4957 (mtmt) cc_final: 0.4623 (tttm) REVERT: C 43 ASP cc_start: 0.7614 (t70) cc_final: 0.7249 (t70) REVERT: C 156 ARG cc_start: 0.7394 (ttp-170) cc_final: 0.7169 (ttt-90) REVERT: C 220 MET cc_start: 0.7724 (mmt) cc_final: 0.7500 (tpt) REVERT: C 441 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6449 (tt0) REVERT: C 481 ARG cc_start: 0.6391 (mtp85) cc_final: 0.6083 (ttt-90) REVERT: C 492 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7385 (mp0) REVERT: C 568 LYS cc_start: 0.7063 (mmtm) cc_final: 0.6841 (mttm) REVERT: D 265 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6361 (mm-30) REVERT: D 275 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7494 (mt-10) REVERT: E 210 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7336 (ttt-90) REVERT: E 265 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6759 (mt-10) REVERT: E 290 ASP cc_start: 0.7444 (t70) cc_final: 0.7033 (t0) REVERT: F 3 LEU cc_start: 0.6595 (mp) cc_final: 0.6307 (mp) REVERT: F 6 LYS cc_start: 0.7689 (tttt) cc_final: 0.6277 (ptpp) REVERT: F 223 LYS cc_start: 0.7137 (mttp) cc_final: 0.6400 (mppt) REVERT: F 318 ASP cc_start: 0.7575 (p0) cc_final: 0.6843 (t0) REVERT: F 363 ASN cc_start: 0.8114 (m-40) cc_final: 0.7672 (t0) REVERT: G 15 ARG cc_start: 0.6629 (mtt180) cc_final: 0.6336 (mtp85) REVERT: G 47 MET cc_start: 0.5561 (ppp) cc_final: 0.5288 (ttp) REVERT: G 148 LYS cc_start: 0.5822 (mtpt) cc_final: 0.5597 (mttm) REVERT: G 177 ARG cc_start: 0.6888 (ttm110) cc_final: 0.6217 (ttt-90) REVERT: G 187 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6798 (mm-30) REVERT: H 87 GLU cc_start: 0.5348 (mp0) cc_final: 0.5043 (mm-30) REVERT: J 81 GLU cc_start: 0.5571 (pp20) cc_final: 0.4968 (tt0) REVERT: J 88 ARG cc_start: 0.5415 (ptm160) cc_final: 0.4789 (tpt-90) REVERT: K 104 MET cc_start: 0.6484 (mtp) cc_final: 0.6040 (tpt) REVERT: L 81 GLU cc_start: 0.6976 (tt0) cc_final: 0.6530 (mt-10) REVERT: L 110 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6990 (mt-10) REVERT: L 142 LEU cc_start: 0.6510 (pt) cc_final: 0.5838 (mt) REVERT: L 160 LYS cc_start: 0.6293 (mmtp) cc_final: 0.5810 (mmpt) REVERT: L 172 ASP cc_start: 0.7596 (t70) cc_final: 0.7132 (m-30) outliers start: 29 outliers final: 22 residues processed: 345 average time/residue: 0.4618 time to fit residues: 245.8953 Evaluate side-chains 317 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 295 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 194 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 281 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 339 optimal weight: 40.0000 chunk 366 optimal weight: 9.9990 chunk 302 optimal weight: 9.9990 chunk 336 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN E 148 GLN F 23 ASN F 323 HIS ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 30114 Z= 0.487 Angle : 0.685 9.456 40813 Z= 0.357 Chirality : 0.050 0.176 4572 Planarity : 0.006 0.076 5333 Dihedral : 6.868 105.317 4259 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.11 % Allowed : 9.76 % Favored : 88.13 % 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: 0.10 (0.13), residues: 3764 helix: 0.69 (0.13), residues: 1541 sheet: -0.20 (0.21), residues: 604 loop : -0.30 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP J 100 HIS 0.008 0.002 HIS A 185 PHE 0.036 0.003 PHE A 230 TYR 0.020 0.002 TYR C 562 ARG 0.007 0.001 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 308 time to evaluate : 3.519 Fit side-chains REVERT: A 17 LYS cc_start: 0.7934 (ptmm) cc_final: 0.7581 (pttp) REVERT: A 43 ASP cc_start: 0.8074 (t0) cc_final: 0.7731 (t70) REVERT: A 85 ASP cc_start: 0.7135 (p0) cc_final: 0.6828 (p0) REVERT: A 124 LYS cc_start: 0.7104 (mptt) cc_final: 0.6821 (mmtm) REVERT: A 180 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: A 329 ARG cc_start: 0.5906 (mtm-85) cc_final: 0.5105 (mmp80) REVERT: A 347 GLU cc_start: 0.6532 (tt0) cc_final: 0.5639 (pm20) REVERT: A 456 GLU cc_start: 0.7370 (tt0) cc_final: 0.6605 (mt-10) REVERT: A 527 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6982 (mm-30) REVERT: A 569 GLU cc_start: 0.5988 (tt0) cc_final: 0.5123 (mm-30) REVERT: B 124 LYS cc_start: 0.6157 (mmtm) cc_final: 0.5923 (ptmt) REVERT: B 177 ASP cc_start: 0.6877 (OUTLIER) cc_final: 0.6608 (p0) REVERT: B 197 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7599 (ttp-110) REVERT: B 410 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.5914 (m-30) REVERT: B 460 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.7352 (ttm170) REVERT: B 474 ASP cc_start: 0.6421 (t0) cc_final: 0.5784 (p0) REVERT: B 509 MET cc_start: 0.7000 (mmt) cc_final: 0.6796 (mmt) REVERT: B 520 LEU cc_start: 0.7255 (mm) cc_final: 0.6960 (mm) REVERT: B 537 ASP cc_start: 0.7055 (p0) cc_final: 0.6227 (m-30) REVERT: B 557 GLU cc_start: 0.6173 (pp20) cc_final: 0.5553 (mt-10) REVERT: C 43 ASP cc_start: 0.7727 (t70) cc_final: 0.7437 (t70) REVERT: C 122 MET cc_start: 0.7596 (ttm) cc_final: 0.7030 (ttm) REVERT: C 156 ARG cc_start: 0.7391 (ttp-170) cc_final: 0.7139 (ttt-90) REVERT: C 480 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6230 (mm-30) REVERT: C 481 ARG cc_start: 0.6434 (mtp85) cc_final: 0.6056 (ttt-90) REVERT: D 61 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: D 128 GLU cc_start: 0.6266 (mm-30) cc_final: 0.5900 (mm-30) REVERT: D 182 GLU cc_start: 0.6216 (tm-30) cc_final: 0.5560 (mm-30) REVERT: D 275 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7572 (mt-10) REVERT: D 434 GLU cc_start: 0.6406 (tt0) cc_final: 0.6033 (tt0) REVERT: E 6 LYS cc_start: 0.6651 (tttt) cc_final: 0.5855 (ptpp) REVERT: E 210 ARG cc_start: 0.7602 (ttp80) cc_final: 0.7312 (ttt-90) REVERT: E 265 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6831 (mt-10) REVERT: E 290 ASP cc_start: 0.7587 (t70) cc_final: 0.6956 (t0) REVERT: E 334 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: F 6 LYS cc_start: 0.7808 (tttt) cc_final: 0.6367 (ptpp) REVERT: F 68 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8300 (mp) REVERT: F 182 GLU cc_start: 0.5562 (OUTLIER) cc_final: 0.5340 (mp0) REVERT: F 223 LYS cc_start: 0.7247 (mttp) cc_final: 0.6429 (mppt) REVERT: F 318 ASP cc_start: 0.7556 (p0) cc_final: 0.6891 (t0) REVERT: F 363 ASN cc_start: 0.8177 (m-40) cc_final: 0.7661 (t0) REVERT: G 17 GLN cc_start: 0.7032 (mm110) cc_final: 0.6728 (mm-40) REVERT: G 47 MET cc_start: 0.5530 (ppp) cc_final: 0.5028 (ttp) REVERT: G 177 ARG cc_start: 0.6968 (ttm110) cc_final: 0.6623 (ttm-80) REVERT: G 187 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6802 (mm-30) REVERT: J 74 GLN cc_start: 0.5125 (tm-30) cc_final: 0.4893 (pt0) REVERT: J 81 GLU cc_start: 0.5461 (pp20) cc_final: 0.4846 (tt0) REVERT: J 88 ARG cc_start: 0.5187 (ptm160) cc_final: 0.4667 (tpt-90) REVERT: J 99 GLU cc_start: 0.5978 (mm-30) cc_final: 0.5544 (mp0) REVERT: K 104 MET cc_start: 0.6537 (mtp) cc_final: 0.6024 (tpt) REVERT: L 100 TRP cc_start: 0.6134 (t-100) cc_final: 0.5261 (t60) REVERT: L 110 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6790 (mt-10) REVERT: L 160 LYS cc_start: 0.6353 (mmtp) cc_final: 0.5701 (mmpt) REVERT: L 172 ASP cc_start: 0.7811 (t70) cc_final: 0.7345 (m-30) outliers start: 65 outliers final: 42 residues processed: 350 average time/residue: 0.4624 time to fit residues: 254.9003 Evaluate side-chains 337 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 288 time to evaluate : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain L residue 68 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 20.0000 chunk 255 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 340 optimal weight: 9.9990 chunk 360 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 322 optimal weight: 0.4980 chunk 97 optimal weight: 9.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN C 238 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN E 148 GLN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30114 Z= 0.268 Angle : 0.545 8.690 40813 Z= 0.282 Chirality : 0.044 0.188 4572 Planarity : 0.005 0.053 5333 Dihedral : 6.380 94.455 4259 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.04 % Allowed : 11.61 % Favored : 86.34 % 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: 0.26 (0.14), residues: 3764 helix: 0.87 (0.14), residues: 1542 sheet: -0.13 (0.21), residues: 600 loop : -0.26 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 100 HIS 0.006 0.001 HIS A 185 PHE 0.021 0.002 PHE A 230 TYR 0.021 0.001 TYR E 13 ARG 0.005 0.000 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 306 time to evaluate : 3.550 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7940 (ptmm) cc_final: 0.7556 (pttp) REVERT: A 43 ASP cc_start: 0.7996 (t0) cc_final: 0.7693 (t70) REVERT: A 124 LYS cc_start: 0.7151 (mptt) cc_final: 0.6758 (mmtm) REVERT: A 329 ARG cc_start: 0.5765 (mtm-85) cc_final: 0.4995 (mmp80) REVERT: A 347 GLU cc_start: 0.6431 (tt0) cc_final: 0.5560 (pm20) REVERT: A 456 GLU cc_start: 0.7509 (tt0) cc_final: 0.6742 (mt-10) REVERT: A 569 GLU cc_start: 0.5960 (tt0) cc_final: 0.5088 (mm-30) REVERT: B 124 LYS cc_start: 0.6032 (mmtm) cc_final: 0.5786 (ptpt) REVERT: B 197 ARG cc_start: 0.7791 (ttp-110) cc_final: 0.7563 (ttp-110) REVERT: B 460 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7225 (ttm170) REVERT: B 474 ASP cc_start: 0.6456 (t0) cc_final: 0.5742 (p0) REVERT: B 516 MET cc_start: 0.6597 (mtm) cc_final: 0.5929 (mtm) REVERT: B 520 LEU cc_start: 0.7365 (mm) cc_final: 0.6896 (mm) REVERT: B 557 GLU cc_start: 0.6201 (pp20) cc_final: 0.5579 (mt-10) REVERT: C 3 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7958 (mt0) REVERT: C 43 ASP cc_start: 0.7686 (t70) cc_final: 0.7411 (t70) REVERT: C 156 ARG cc_start: 0.7343 (ttp-170) cc_final: 0.7081 (ttt-90) REVERT: C 480 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6198 (mm-30) REVERT: C 481 ARG cc_start: 0.6430 (mtp85) cc_final: 0.6020 (ttt-90) REVERT: C 534 VAL cc_start: 0.6221 (m) cc_final: 0.5969 (p) REVERT: D 182 GLU cc_start: 0.6326 (tm-30) cc_final: 0.5728 (mm-30) REVERT: D 206 GLN cc_start: 0.7272 (mm-40) cc_final: 0.6589 (pp30) REVERT: D 265 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6448 (mm-30) REVERT: D 275 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7722 (mt-10) REVERT: E 210 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7219 (ttt-90) REVERT: E 265 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6735 (mt-10) REVERT: E 334 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: F 3 LEU cc_start: 0.6665 (mp) cc_final: 0.6357 (mp) REVERT: F 6 LYS cc_start: 0.7784 (tttt) cc_final: 0.6376 (ptpp) REVERT: F 182 GLU cc_start: 0.5593 (OUTLIER) cc_final: 0.5115 (mp0) REVERT: F 318 ASP cc_start: 0.7552 (p0) cc_final: 0.6949 (t0) REVERT: F 363 ASN cc_start: 0.8146 (m-40) cc_final: 0.7617 (t0) REVERT: G 15 ARG cc_start: 0.6657 (mtt180) cc_final: 0.6320 (mtp85) REVERT: G 17 GLN cc_start: 0.7069 (mm110) cc_final: 0.6729 (mm-40) REVERT: G 47 MET cc_start: 0.5511 (ppp) cc_final: 0.5103 (ttp) REVERT: G 177 ARG cc_start: 0.6919 (ttm170) cc_final: 0.6576 (ttm-80) REVERT: G 187 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6678 (mm-30) REVERT: J 74 GLN cc_start: 0.5089 (tm-30) cc_final: 0.4882 (pt0) REVERT: J 88 ARG cc_start: 0.4885 (ptm160) cc_final: 0.4429 (tmm-80) REVERT: J 99 GLU cc_start: 0.5946 (mm-30) cc_final: 0.5497 (mp0) REVERT: J 105 ARG cc_start: 0.6661 (ttm170) cc_final: 0.6424 (ttm-80) REVERT: K 104 MET cc_start: 0.6447 (mtp) cc_final: 0.6008 (tpt) REVERT: L 100 TRP cc_start: 0.6135 (t-100) cc_final: 0.5637 (t60) REVERT: L 110 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6834 (mt-10) REVERT: L 160 LYS cc_start: 0.6280 (mmtp) cc_final: 0.5630 (mmpt) REVERT: L 172 ASP cc_start: 0.7855 (t70) cc_final: 0.7386 (m-30) outliers start: 63 outliers final: 38 residues processed: 341 average time/residue: 0.4621 time to fit residues: 245.9424 Evaluate side-chains 331 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 290 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 176 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 148 optimal weight: 0.0670 chunk 307 optimal weight: 9.9990 chunk 249 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 184 optimal weight: 0.3980 chunk 323 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 437 GLN E 407 ASN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30114 Z= 0.187 Angle : 0.492 7.760 40813 Z= 0.253 Chirality : 0.042 0.172 4572 Planarity : 0.004 0.053 5333 Dihedral : 6.016 83.106 4259 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.24 % Allowed : 12.39 % Favored : 85.37 % 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: 0.53 (0.14), residues: 3764 helix: 1.13 (0.14), residues: 1541 sheet: -0.04 (0.21), residues: 597 loop : -0.14 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 100 HIS 0.005 0.001 HIS A 185 PHE 0.015 0.001 PHE A 230 TYR 0.019 0.001 TYR E 13 ARG 0.004 0.000 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 311 time to evaluate : 3.525 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7971 (ptmm) cc_final: 0.7588 (pttp) REVERT: A 43 ASP cc_start: 0.7907 (t0) cc_final: 0.7615 (t70) REVERT: A 85 ASP cc_start: 0.7213 (p0) cc_final: 0.6829 (p0) REVERT: A 124 LYS cc_start: 0.7148 (mptt) cc_final: 0.6914 (tppt) REVERT: A 329 ARG cc_start: 0.5609 (mtm-85) cc_final: 0.5005 (mmp80) REVERT: A 347 GLU cc_start: 0.6380 (tt0) cc_final: 0.5480 (pm20) REVERT: A 456 GLU cc_start: 0.7491 (tt0) cc_final: 0.6720 (mt-10) REVERT: A 481 ARG cc_start: 0.7061 (mmm-85) cc_final: 0.6753 (mtp85) REVERT: A 527 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6915 (mm-30) REVERT: A 569 GLU cc_start: 0.5941 (tt0) cc_final: 0.5006 (mm-30) REVERT: B 124 LYS cc_start: 0.6026 (mmtm) cc_final: 0.5729 (ptpt) REVERT: B 197 ARG cc_start: 0.7841 (ttp-110) cc_final: 0.7609 (ttp-110) REVERT: B 460 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7268 (ttm170) REVERT: B 474 ASP cc_start: 0.6534 (t0) cc_final: 0.5809 (p0) REVERT: B 516 MET cc_start: 0.6609 (mtm) cc_final: 0.5985 (mtm) REVERT: B 520 LEU cc_start: 0.7464 (mm) cc_final: 0.7029 (mm) REVERT: C 43 ASP cc_start: 0.7646 (t70) cc_final: 0.7308 (t70) REVERT: C 156 ARG cc_start: 0.7323 (ttp-170) cc_final: 0.7059 (ttt-90) REVERT: C 480 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6209 (mm-30) REVERT: C 481 ARG cc_start: 0.6466 (mtp85) cc_final: 0.6058 (ttt-90) REVERT: C 534 VAL cc_start: 0.6198 (m) cc_final: 0.5927 (p) REVERT: D 275 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7600 (mt-10) REVERT: E 210 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7178 (ttt-90) REVERT: E 265 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6737 (mt-10) REVERT: E 275 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7220 (mt-10) REVERT: F 3 LEU cc_start: 0.6666 (mp) cc_final: 0.6351 (mp) REVERT: F 6 LYS cc_start: 0.7770 (tttt) cc_final: 0.6366 (ptpp) REVERT: F 182 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5240 (mp0) REVERT: F 318 ASP cc_start: 0.7530 (p0) cc_final: 0.6969 (t0) REVERT: F 363 ASN cc_start: 0.8110 (m-40) cc_final: 0.7588 (t0) REVERT: G 15 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6377 (mtp85) REVERT: G 47 MET cc_start: 0.5615 (ppp) cc_final: 0.5237 (ttp) REVERT: G 177 ARG cc_start: 0.6878 (ttm170) cc_final: 0.6550 (ttm-80) REVERT: G 187 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6684 (mm-30) REVERT: J 88 ARG cc_start: 0.4877 (ptm160) cc_final: 0.4352 (tmm-80) REVERT: J 105 ARG cc_start: 0.6625 (ttm170) cc_final: 0.6365 (ttm-80) REVERT: K 104 MET cc_start: 0.6378 (mtp) cc_final: 0.5878 (tpt) REVERT: L 100 TRP cc_start: 0.6199 (t-100) cc_final: 0.5648 (t60) REVERT: L 110 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6845 (mt-10) REVERT: L 160 LYS cc_start: 0.6240 (mmtp) cc_final: 0.5562 (mmpt) REVERT: L 172 ASP cc_start: 0.7841 (t70) cc_final: 0.7368 (m-30) outliers start: 69 outliers final: 50 residues processed: 358 average time/residue: 0.4323 time to fit residues: 243.1857 Evaluate side-chains 347 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 296 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 112 LEU 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: 10.0000 chunk 211 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 360 optimal weight: 0.6980 chunk 299 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN E 148 GLN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30114 Z= 0.339 Angle : 0.577 8.238 40813 Z= 0.296 Chirality : 0.046 0.165 4572 Planarity : 0.005 0.064 5333 Dihedral : 6.194 81.147 4259 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.28 % Allowed : 12.36 % Favored : 84.37 % 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: 0.25 (0.14), residues: 3764 helix: 0.88 (0.14), residues: 1541 sheet: -0.17 (0.21), residues: 603 loop : -0.27 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 100 HIS 0.007 0.001 HIS A 185 PHE 0.029 0.002 PHE A 230 TYR 0.018 0.002 TYR E 13 ARG 0.005 0.000 ARG G 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 297 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7935 (ptmm) cc_final: 0.7540 (pttp) REVERT: A 85 ASP cc_start: 0.7242 (p0) cc_final: 0.6927 (p0) REVERT: A 124 LYS cc_start: 0.7020 (mptt) cc_final: 0.6650 (mmtm) REVERT: A 180 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: A 329 ARG cc_start: 0.5775 (mtm-85) cc_final: 0.5077 (mmp80) REVERT: A 347 GLU cc_start: 0.6428 (tt0) cc_final: 0.5569 (pm20) REVERT: A 456 GLU cc_start: 0.7529 (tt0) cc_final: 0.6729 (mt-10) REVERT: A 466 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6290 (mt-10) REVERT: A 481 ARG cc_start: 0.7068 (mmm-85) cc_final: 0.6758 (mtp85) REVERT: A 527 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6945 (mm-30) REVERT: A 565 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: B 124 LYS cc_start: 0.6092 (mmtm) cc_final: 0.5794 (ptpt) REVERT: B 197 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.7585 (ttp-110) REVERT: B 384 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7741 (p) REVERT: B 460 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7316 (ttm170) REVERT: B 474 ASP cc_start: 0.6514 (t0) cc_final: 0.5873 (p0) REVERT: B 485 GLU cc_start: 0.6671 (mm-30) cc_final: 0.5693 (tp30) REVERT: B 520 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7028 (mm) REVERT: C 43 ASP cc_start: 0.7698 (t70) cc_final: 0.7398 (t70) REVERT: C 156 ARG cc_start: 0.7355 (ttp-170) cc_final: 0.7078 (ttt-90) REVERT: C 480 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6168 (mm-30) REVERT: C 481 ARG cc_start: 0.6492 (mtp85) cc_final: 0.6065 (ttt-90) REVERT: C 534 VAL cc_start: 0.6129 (m) cc_final: 0.5857 (p) REVERT: D 61 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: D 206 GLN cc_start: 0.7253 (mm-40) cc_final: 0.6558 (pp30) REVERT: D 265 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6824 (mp0) REVERT: D 275 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7562 (mt-10) REVERT: D 331 TYR cc_start: 0.7011 (m-80) cc_final: 0.6806 (m-80) REVERT: D 434 GLU cc_start: 0.6449 (tt0) cc_final: 0.6126 (tt0) REVERT: E 210 ARG cc_start: 0.7652 (ttp80) cc_final: 0.7286 (ttt-90) REVERT: E 265 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6793 (mt-10) REVERT: E 275 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7213 (mt-10) REVERT: E 334 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: E 362 MET cc_start: 0.8974 (ttt) cc_final: 0.8651 (ttt) REVERT: E 407 ASN cc_start: 0.4371 (OUTLIER) cc_final: 0.3965 (t0) REVERT: F 3 LEU cc_start: 0.6737 (mp) cc_final: 0.6479 (mp) REVERT: F 6 LYS cc_start: 0.7835 (tttt) cc_final: 0.6333 (ptpp) REVERT: F 182 GLU cc_start: 0.5744 (OUTLIER) cc_final: 0.5288 (mp0) REVERT: F 318 ASP cc_start: 0.7526 (p0) cc_final: 0.7028 (t0) REVERT: F 363 ASN cc_start: 0.8166 (m-40) cc_final: 0.7614 (t0) REVERT: G 47 MET cc_start: 0.5486 (ppp) cc_final: 0.5089 (ttp) REVERT: G 177 ARG cc_start: 0.6922 (ttm170) cc_final: 0.6592 (ttm-80) REVERT: G 187 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6687 (mm-30) REVERT: J 88 ARG cc_start: 0.4835 (ptm160) cc_final: 0.4339 (tmm-80) REVERT: J 105 ARG cc_start: 0.6622 (ttm170) cc_final: 0.6387 (ttm-80) REVERT: K 104 MET cc_start: 0.6496 (mtp) cc_final: 0.5925 (tpt) REVERT: L 100 TRP cc_start: 0.6020 (OUTLIER) cc_final: 0.5469 (t60) REVERT: L 110 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6731 (mt-10) REVERT: L 160 LYS cc_start: 0.6365 (mmtp) cc_final: 0.5728 (mmpt) REVERT: L 172 ASP cc_start: 0.7832 (t70) cc_final: 0.7351 (m-30) outliers start: 101 outliers final: 73 residues processed: 368 average time/residue: 0.4168 time to fit residues: 241.3022 Evaluate side-chains 375 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 293 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 100 TRP Chi-restraints excluded: chain L residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 303 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 359 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN E 148 GLN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30114 Z= 0.275 Angle : 0.541 8.434 40813 Z= 0.278 Chirality : 0.044 0.171 4572 Planarity : 0.005 0.058 5333 Dihedral : 6.117 77.485 4259 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.18 % Allowed : 12.91 % Favored : 83.91 % 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: 0.28 (0.14), residues: 3764 helix: 0.91 (0.14), residues: 1540 sheet: -0.14 (0.21), residues: 600 loop : -0.27 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 100 HIS 0.006 0.001 HIS A 185 PHE 0.022 0.002 PHE A 230 TYR 0.018 0.001 TYR E 13 ARG 0.004 0.000 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 297 time to evaluate : 3.345 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7921 (ptmm) cc_final: 0.7536 (pttp) REVERT: A 124 LYS cc_start: 0.6997 (mptt) cc_final: 0.6783 (tppt) REVERT: A 180 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7438 (pm20) REVERT: A 294 MET cc_start: 0.7824 (mtt) cc_final: 0.7499 (mtt) REVERT: A 329 ARG cc_start: 0.5761 (mtm-85) cc_final: 0.5076 (mmp80) REVERT: A 347 GLU cc_start: 0.6418 (tt0) cc_final: 0.5460 (pm20) REVERT: A 456 GLU cc_start: 0.7527 (tt0) cc_final: 0.6720 (mt-10) REVERT: A 481 ARG cc_start: 0.7072 (mmm-85) cc_final: 0.6772 (mtp85) REVERT: A 527 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6953 (mm-30) REVERT: A 565 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: B 197 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7579 (ttp-110) REVERT: B 323 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7606 (mtp) REVERT: B 384 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7772 (p) REVERT: B 460 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.7216 (ttm170) REVERT: B 474 ASP cc_start: 0.6628 (t0) cc_final: 0.5894 (p0) REVERT: B 485 GLU cc_start: 0.6838 (mm-30) cc_final: 0.5880 (tp30) REVERT: B 520 LEU cc_start: 0.7543 (mm) cc_final: 0.7142 (mm) REVERT: B 557 GLU cc_start: 0.6064 (pp20) cc_final: 0.5474 (mt-10) REVERT: C 43 ASP cc_start: 0.7699 (t70) cc_final: 0.7402 (t70) REVERT: C 156 ARG cc_start: 0.7309 (ttp-170) cc_final: 0.7024 (ttt-90) REVERT: C 480 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6151 (mm-30) REVERT: C 481 ARG cc_start: 0.6542 (mtp85) cc_final: 0.6077 (ttt-90) REVERT: C 534 VAL cc_start: 0.6203 (m) cc_final: 0.5942 (p) REVERT: D 206 GLN cc_start: 0.7296 (mm-40) cc_final: 0.6597 (pp30) REVERT: D 265 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6797 (mp0) REVERT: D 275 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7652 (mt-10) REVERT: D 331 TYR cc_start: 0.7043 (m-80) cc_final: 0.6794 (m-80) REVERT: D 434 GLU cc_start: 0.6419 (tt0) cc_final: 0.6082 (tt0) REVERT: E 210 ARG cc_start: 0.7642 (ttp80) cc_final: 0.7282 (ttt-90) REVERT: E 265 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6773 (mt-10) REVERT: E 275 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7225 (mt-10) REVERT: E 277 ILE cc_start: 0.8612 (mm) cc_final: 0.8231 (tp) REVERT: E 334 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: E 407 ASN cc_start: 0.4311 (OUTLIER) cc_final: 0.3919 (t0) REVERT: F 6 LYS cc_start: 0.7820 (tttt) cc_final: 0.6383 (ptpp) REVERT: F 182 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5564 (mp0) REVERT: F 318 ASP cc_start: 0.7509 (p0) cc_final: 0.7009 (t0) REVERT: F 363 ASN cc_start: 0.8173 (m-40) cc_final: 0.7619 (t0) REVERT: G 17 GLN cc_start: 0.7080 (mm110) cc_final: 0.6769 (mm-40) REVERT: G 47 MET cc_start: 0.5443 (ppp) cc_final: 0.5028 (ttp) REVERT: G 177 ARG cc_start: 0.6912 (ttm170) cc_final: 0.6586 (ttm-80) REVERT: G 187 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6687 (mm-30) REVERT: J 88 ARG cc_start: 0.4790 (ptm160) cc_final: 0.4296 (tmm-80) REVERT: J 99 GLU cc_start: 0.5801 (mm-30) cc_final: 0.5411 (mp0) REVERT: J 105 ARG cc_start: 0.6702 (ttm170) cc_final: 0.6451 (ttm-80) REVERT: K 104 MET cc_start: 0.6466 (mtp) cc_final: 0.5913 (tpt) REVERT: L 100 TRP cc_start: 0.6111 (OUTLIER) cc_final: 0.5588 (t60) REVERT: L 110 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6713 (mt-10) REVERT: L 160 LYS cc_start: 0.6357 (mmtp) cc_final: 0.5720 (mmpt) REVERT: L 172 ASP cc_start: 0.7797 (t70) cc_final: 0.7322 (m-30) outliers start: 98 outliers final: 77 residues processed: 364 average time/residue: 0.4055 time to fit residues: 234.6525 Evaluate side-chains 378 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 293 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 100 TRP Chi-restraints excluded: chain L residue 112 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 228 optimal weight: 0.0770 chunk 244 optimal weight: 10.0000 chunk 177 optimal weight: 0.0770 chunk 33 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30114 Z= 0.165 Angle : 0.478 8.809 40813 Z= 0.244 Chirality : 0.042 0.172 4572 Planarity : 0.004 0.058 5333 Dihedral : 5.821 73.459 4259 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.17 % Allowed : 14.01 % Favored : 83.81 % 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: 0.58 (0.14), residues: 3764 helix: 1.17 (0.14), residues: 1554 sheet: 0.06 (0.22), residues: 557 loop : -0.14 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 100 HIS 0.005 0.001 HIS A 185 PHE 0.014 0.001 PHE C 230 TYR 0.022 0.001 TYR E 13 ARG 0.003 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 304 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7924 (ptmm) cc_final: 0.7549 (pttp) REVERT: A 85 ASP cc_start: 0.7174 (p0) cc_final: 0.6776 (p0) REVERT: A 124 LYS cc_start: 0.7076 (mptt) cc_final: 0.6773 (tppt) REVERT: A 329 ARG cc_start: 0.5488 (mtm-85) cc_final: 0.4972 (mmp80) REVERT: A 347 GLU cc_start: 0.6332 (tt0) cc_final: 0.5646 (pm20) REVERT: A 456 GLU cc_start: 0.7557 (tt0) cc_final: 0.6760 (mt-10) REVERT: A 481 ARG cc_start: 0.7086 (mmm-85) cc_final: 0.6805 (mtp85) REVERT: A 527 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6948 (mm-30) REVERT: B 124 LYS cc_start: 0.6115 (mmtt) cc_final: 0.5363 (mtpp) REVERT: B 159 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7474 (mm-30) REVERT: B 197 ARG cc_start: 0.7910 (ttp-110) cc_final: 0.7659 (ttp-110) REVERT: B 323 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7628 (mtp) REVERT: B 460 ARG cc_start: 0.7544 (ttm-80) cc_final: 0.7177 (ttm170) REVERT: B 474 ASP cc_start: 0.6636 (t0) cc_final: 0.5827 (p0) REVERT: B 485 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6111 (pt0) REVERT: B 520 LEU cc_start: 0.7493 (mm) cc_final: 0.7175 (mm) REVERT: B 557 GLU cc_start: 0.5840 (pp20) cc_final: 0.5369 (mt-10) REVERT: C 3 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: C 43 ASP cc_start: 0.7629 (t70) cc_final: 0.7316 (t70) REVERT: C 156 ARG cc_start: 0.7279 (ttp-170) cc_final: 0.7008 (ttt-90) REVERT: C 261 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7776 (mm-30) REVERT: C 480 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6166 (mm-30) REVERT: C 481 ARG cc_start: 0.6548 (mtp85) cc_final: 0.6083 (ttt-90) REVERT: C 534 VAL cc_start: 0.6134 (m) cc_final: 0.5858 (p) REVERT: D 206 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6606 (pp30) REVERT: D 265 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6838 (mp0) REVERT: D 275 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7322 (mm-30) REVERT: D 331 TYR cc_start: 0.7069 (m-80) cc_final: 0.6772 (m-80) REVERT: E 210 ARG cc_start: 0.7605 (ttp80) cc_final: 0.7235 (ttt-90) REVERT: E 265 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6749 (mt-10) REVERT: E 275 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7206 (mt-10) REVERT: E 334 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: E 362 MET cc_start: 0.8939 (ttt) cc_final: 0.8654 (ttt) REVERT: F 6 LYS cc_start: 0.7766 (tttt) cc_final: 0.6331 (ptpp) REVERT: F 182 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5613 (mp0) REVERT: F 318 ASP cc_start: 0.7581 (p0) cc_final: 0.7000 (t0) REVERT: F 363 ASN cc_start: 0.8157 (m-40) cc_final: 0.7599 (t0) REVERT: G 15 ARG cc_start: 0.6699 (mtt180) cc_final: 0.6355 (mtp85) REVERT: G 17 GLN cc_start: 0.7119 (mm110) cc_final: 0.6682 (mm-40) REVERT: G 19 ARG cc_start: 0.6857 (ttm110) cc_final: 0.6378 (ttm110) REVERT: G 47 MET cc_start: 0.5562 (ppp) cc_final: 0.5232 (ttp) REVERT: G 177 ARG cc_start: 0.6875 (ttm170) cc_final: 0.6564 (ttm-80) REVERT: G 187 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6719 (mm-30) REVERT: J 88 ARG cc_start: 0.4824 (ptm160) cc_final: 0.4312 (tmm-80) REVERT: J 99 GLU cc_start: 0.5729 (mm-30) cc_final: 0.5373 (mp0) REVERT: K 104 MET cc_start: 0.6356 (mtp) cc_final: 0.5932 (tpt) REVERT: L 100 TRP cc_start: 0.6058 (t-100) cc_final: 0.5562 (t60) REVERT: L 110 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6706 (mt-10) REVERT: L 160 LYS cc_start: 0.6263 (mmtp) cc_final: 0.5613 (mmpt) REVERT: L 172 ASP cc_start: 0.7784 (t70) cc_final: 0.7313 (m-30) outliers start: 67 outliers final: 56 residues processed: 347 average time/residue: 0.4532 time to fit residues: 246.7819 Evaluate side-chains 359 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 299 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 112 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 335 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 316 optimal weight: 7.9990 chunk 333 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 418 HIS C 496 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN E 142 ASN E 148 GLN H 82 GLN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 30114 Z= 0.505 Angle : 0.689 10.043 40813 Z= 0.355 Chirality : 0.050 0.187 4572 Planarity : 0.006 0.089 5333 Dihedral : 6.426 79.472 4259 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.98 % Allowed : 13.43 % Favored : 83.59 % 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: -0.09 (0.13), residues: 3764 helix: 0.58 (0.13), residues: 1532 sheet: -0.26 (0.21), residues: 604 loop : -0.47 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 100 HIS 0.010 0.002 HIS L 130 PHE 0.041 0.003 PHE A 230 TYR 0.020 0.003 TYR C 562 ARG 0.008 0.001 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 296 time to evaluate : 3.679 Fit side-chains revert: symmetry clash REVERT: A 85 ASP cc_start: 0.7288 (p0) cc_final: 0.6840 (p0) REVERT: A 124 LYS cc_start: 0.6968 (mptt) cc_final: 0.6617 (mmtm) REVERT: A 180 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7402 (pm20) REVERT: A 329 ARG cc_start: 0.5986 (mtm-85) cc_final: 0.5192 (mmp80) REVERT: A 347 GLU cc_start: 0.6559 (tt0) cc_final: 0.5656 (pm20) REVERT: A 456 GLU cc_start: 0.7647 (tt0) cc_final: 0.6790 (mt-10) REVERT: B 124 LYS cc_start: 0.6216 (mmtt) cc_final: 0.5453 (mtpp) REVERT: B 323 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7618 (mtp) REVERT: B 410 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.5998 (m-30) REVERT: B 460 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7327 (ttm170) REVERT: B 520 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7096 (mm) REVERT: C 43 ASP cc_start: 0.7749 (t70) cc_final: 0.7469 (t70) REVERT: C 154 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7270 (mtm180) REVERT: C 156 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.7095 (ttt-90) REVERT: C 480 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6174 (mm-30) REVERT: C 481 ARG cc_start: 0.6617 (mtp85) cc_final: 0.6239 (ttt-90) REVERT: C 534 VAL cc_start: 0.6266 (m) cc_final: 0.6027 (p) REVERT: D 61 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: D 274 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.5276 (mpt-90) REVERT: D 275 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7624 (mt-10) REVERT: D 331 TYR cc_start: 0.7180 (m-80) cc_final: 0.6934 (m-80) REVERT: D 434 GLU cc_start: 0.6513 (tt0) cc_final: 0.6196 (tt0) REVERT: E 210 ARG cc_start: 0.7631 (ttp80) cc_final: 0.7392 (ttt-90) REVERT: E 265 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6802 (mt-10) REVERT: E 275 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7252 (mt-10) REVERT: E 277 ILE cc_start: 0.8713 (mm) cc_final: 0.8324 (tp) REVERT: E 290 ASP cc_start: 0.7537 (t70) cc_final: 0.6903 (t0) REVERT: E 334 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: E 407 ASN cc_start: 0.4631 (OUTLIER) cc_final: 0.4248 (t0) REVERT: F 6 LYS cc_start: 0.7853 (tttt) cc_final: 0.6418 (mttt) REVERT: F 318 ASP cc_start: 0.7491 (p0) cc_final: 0.7014 (t0) REVERT: F 363 ASN cc_start: 0.8242 (m-40) cc_final: 0.7650 (t0) REVERT: F 398 ILE cc_start: 0.7456 (mt) cc_final: 0.7183 (mm) REVERT: G 47 MET cc_start: 0.5497 (ppp) cc_final: 0.5057 (ttp) REVERT: G 177 ARG cc_start: 0.7004 (ttm170) cc_final: 0.6715 (ttm-80) REVERT: G 187 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6688 (mm-30) REVERT: J 88 ARG cc_start: 0.4871 (ptm160) cc_final: 0.4287 (tmm-80) REVERT: K 104 MET cc_start: 0.6463 (mtp) cc_final: 0.6050 (tpt) REVERT: L 100 TRP cc_start: 0.6131 (t-100) cc_final: 0.5534 (t60) REVERT: L 160 LYS cc_start: 0.6407 (mmtp) cc_final: 0.5794 (mmpt) REVERT: L 172 ASP cc_start: 0.7829 (t70) cc_final: 0.7369 (m-30) outliers start: 92 outliers final: 75 residues processed: 362 average time/residue: 0.4347 time to fit residues: 248.4635 Evaluate side-chains 369 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 286 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 246 optimal weight: 0.6980 chunk 371 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 295 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 228 optimal weight: 0.1980 chunk 181 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 437 GLN E 148 GLN H 82 GLN J 74 GLN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 30114 Z= 0.138 Angle : 0.482 8.766 40813 Z= 0.247 Chirality : 0.042 0.176 4572 Planarity : 0.004 0.063 5333 Dihedral : 5.835 73.653 4259 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.01 % Allowed : 14.60 % Favored : 83.39 % 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: 0.50 (0.14), residues: 3764 helix: 1.10 (0.14), residues: 1546 sheet: 0.07 (0.22), residues: 564 loop : -0.19 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 100 HIS 0.005 0.001 HIS C 418 PHE 0.014 0.001 PHE C 230 TYR 0.023 0.001 TYR E 13 ARG 0.005 0.000 ARG B 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 301 time to evaluate : 3.583 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7939 (ptmm) cc_final: 0.7555 (pttp) REVERT: A 85 ASP cc_start: 0.7196 (p0) cc_final: 0.6783 (p0) REVERT: A 124 LYS cc_start: 0.7102 (mptt) cc_final: 0.6796 (tppt) REVERT: A 294 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7236 (mtt) REVERT: A 329 ARG cc_start: 0.5552 (mtm-85) cc_final: 0.5030 (mmp80) REVERT: A 347 GLU cc_start: 0.6339 (tt0) cc_final: 0.5610 (pm20) REVERT: A 456 GLU cc_start: 0.7578 (tt0) cc_final: 0.6761 (mt-10) REVERT: A 481 ARG cc_start: 0.7035 (mmm-85) cc_final: 0.6783 (mtp85) REVERT: A 509 MET cc_start: 0.7978 (mmm) cc_final: 0.7744 (mmm) REVERT: A 527 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6944 (mm-30) REVERT: A 565 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: B 124 LYS cc_start: 0.6023 (mmtt) cc_final: 0.5258 (mtpp) REVERT: B 159 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7483 (mm-30) REVERT: B 323 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7624 (mtp) REVERT: B 384 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7769 (p) REVERT: B 460 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7267 (ttm170) REVERT: B 474 ASP cc_start: 0.6606 (t0) cc_final: 0.5732 (p0) REVERT: B 485 GLU cc_start: 0.6582 (mm-30) cc_final: 0.5649 (tp30) REVERT: B 520 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7186 (mm) REVERT: C 43 ASP cc_start: 0.7629 (t70) cc_final: 0.7333 (t70) REVERT: C 154 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7205 (mtm180) REVERT: C 156 ARG cc_start: 0.7244 (ttp-170) cc_final: 0.6980 (ttt-90) REVERT: C 480 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6150 (mm-30) REVERT: C 481 ARG cc_start: 0.6529 (mtp85) cc_final: 0.6042 (ttt-90) REVERT: C 492 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7461 (mp0) REVERT: C 534 VAL cc_start: 0.6278 (m) cc_final: 0.6034 (p) REVERT: D 206 GLN cc_start: 0.7157 (mm-40) cc_final: 0.6500 (pp30) REVERT: D 265 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6805 (mp0) REVERT: D 275 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7235 (mm-30) REVERT: D 331 TYR cc_start: 0.7053 (m-80) cc_final: 0.6763 (m-80) REVERT: E 210 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7237 (ttt-90) REVERT: E 265 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6721 (mt-10) REVERT: E 275 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7178 (mt-10) REVERT: E 334 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: E 362 MET cc_start: 0.8872 (ttt) cc_final: 0.8649 (ttt) REVERT: F 6 LYS cc_start: 0.7795 (tttt) cc_final: 0.6350 (ptpp) REVERT: F 318 ASP cc_start: 0.7570 (p0) cc_final: 0.6974 (t0) REVERT: G 15 ARG cc_start: 0.6683 (mtt180) cc_final: 0.6170 (mtp85) REVERT: G 17 GLN cc_start: 0.7071 (mm110) cc_final: 0.6689 (mm-40) REVERT: G 19 ARG cc_start: 0.6859 (ttm110) cc_final: 0.6072 (mtt90) REVERT: G 47 MET cc_start: 0.5566 (ppp) cc_final: 0.5233 (ttp) REVERT: G 177 ARG cc_start: 0.6906 (ttm170) cc_final: 0.6549 (ttm-80) REVERT: G 181 GLN cc_start: 0.7696 (mt0) cc_final: 0.7464 (mt0) REVERT: G 187 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6689 (mm-30) REVERT: J 88 ARG cc_start: 0.4838 (ptm160) cc_final: 0.4300 (tmm-80) REVERT: K 104 MET cc_start: 0.6340 (mtp) cc_final: 0.5841 (tpt) REVERT: L 100 TRP cc_start: 0.6220 (OUTLIER) cc_final: 0.5616 (t60) REVERT: L 110 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6872 (mt-10) REVERT: L 160 LYS cc_start: 0.6229 (mmtp) cc_final: 0.5604 (mmpt) REVERT: L 172 ASP cc_start: 0.7793 (t70) cc_final: 0.7359 (m-30) outliers start: 62 outliers final: 47 residues processed: 342 average time/residue: 0.4593 time to fit residues: 245.1644 Evaluate side-chains 348 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 294 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 100 TRP Chi-restraints excluded: chain L residue 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 10.0000 chunk 315 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 296 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 304 optimal weight: 0.0770 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 overall best weight: 3.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100859 restraints weight = 42814.631| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.31 r_work: 0.2969 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30114 Z= 0.234 Angle : 0.518 8.963 40813 Z= 0.264 Chirality : 0.043 0.178 4572 Planarity : 0.005 0.057 5333 Dihedral : 5.869 72.531 4259 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.95 % Allowed : 14.82 % Favored : 83.23 % 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: 3764 helix: 1.09 (0.14), residues: 1544 sheet: 0.03 (0.22), residues: 556 loop : -0.24 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 100 HIS 0.006 0.001 HIS A 185 PHE 0.021 0.002 PHE A 230 TYR 0.019 0.001 TYR E 13 ARG 0.006 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6466.93 seconds wall clock time: 117 minutes 13.80 seconds (7033.80 seconds total)