Starting phenix.real_space_refine on Wed Feb 21 03:54:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/02_2024/7val_31849_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/02_2024/7val_31849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/02_2024/7val_31849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/02_2024/7val_31849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/02_2024/7val_31849_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/02_2024/7val_31849_updated.pdb" } resolution = 3.1 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= 0.007 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 53": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "E TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 207": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: 14.72, per 1000 atoms: 0.50 Number of scatterers: 29558 At special positions: 0 Unit cell: (151.36, 148.72, 178.64, 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.27 Conformation dependent library (CDL) restraints added in 5.0 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: 136 helices and 36 sheets defined 42.7% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.07 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 315 removed outlier: 3.663A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.315A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.630A 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 400 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.997A 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) removed outlier: 3.540A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 541 removed outlier: 5.087A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 4.937A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.687A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.955A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 364 removed outlier: 4.231A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 470 removed outlier: 3.878A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 478 through 493 removed outlier: 3.568A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.683A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.539A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 271 removed outlier: 3.553A 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: 3.578A 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 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.988A 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: 3.607A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 414 No H-bonds generated for 'chain 'C' and resid 411 through 414' Processing helix chain 'C' and resid 433 through 442 removed outlier: 3.775A pdb=" N ASP C 436 " --> pdb=" O SER C 433 " (cutoff:3.500A) Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 447 through 471 removed outlier: 3.930A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 531 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 559 through 577 removed outlier: 3.547A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 198 through 211 removed outlier: 4.114A 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 274 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 285 through 297 removed outlier: 4.468A pdb=" N TYR D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU D 296 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 297 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 removed outlier: 3.597A pdb=" N TYR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.889A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.879A 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 467 through 473 removed outlier: 3.614A pdb=" N TRP D 471 " --> pdb=" O GLU D 468 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLY D 472 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.852A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 285 through 297 removed outlier: 4.398A pdb=" N TYR E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU E 296 " --> 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 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 375 through 399 removed outlier: 4.174A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 445 removed outlier: 3.900A 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 '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 229 through 249 removed outlier: 3.837A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.611A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.080A 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 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.682A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) 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: 3.550A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.838A 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: 3.984A 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 'G' and resid 8 through 70 removed outlier: 3.814A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 123 through 207 removed outlier: 3.797A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 7 through 15 Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.779A pdb=" N LEU H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 63 removed outlier: 6.125A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 4.037A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 77 through 82' Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 82 through 118 removed outlier: 3.698A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 92 removed outlier: 4.126A pdb=" N LEU J 67 " --> pdb=" O ALA J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 100 through 114 Processing helix chain 'J' and resid 125 through 138 Proline residue: J 129 - end of helix removed outlier: 4.357A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.788A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 4.061A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 96 removed outlier: 3.981A pdb=" N ALA L 93 " --> pdb=" O GLU L 89 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Proline residue: L 95 - end of helix Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix removed outlier: 3.561A pdb=" N ARG L 105 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 138 removed outlier: 3.721A pdb=" N GLU L 132 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA L 133 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU L 134 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA L 135 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 5.323A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.484A 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: 6.593A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.566A 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: 4.129A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 249 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= E, first strand: chain 'A' and resid 197 through 199 removed outlier: 4.657A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.605A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.019A 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: 6.636A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.734A 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 76 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 405 through 407 removed outlier: 8.659A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP B 325 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 253 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 366 through 369 Processing sheet with id= M, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.883A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.789A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.502A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= Q, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.083A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 117 through 119 removed outlier: 3.538A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 197 through 199 removed outlier: 3.670A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS C 367 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.679A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.927A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.417A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.785A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.991A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Z, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.630A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= AB, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.971A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.468A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.536A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 92 through 94 removed outlier: 8.297A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.865A 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 91 through 96 Processing sheet with id= AH, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.539A pdb=" N ALA H 5 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 141 through 144 removed outlier: 6.750A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.547A pdb=" N GLU L 141 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL L 155 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU L 121 " --> pdb=" O ARG L 153 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG L 153 " --> pdb=" O LEU L 121 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3267 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: 9.95 Time building geometry restraints manager: 12.16 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: 9953 1.34 - 1.46: 4219 1.46 - 1.57: 15736 1.57 - 1.69: 12 1.69 - 1.81: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.512 0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.513 0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.513 0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.513 0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" C MET F 445 " pdb=" N LEU F 446 " ideal model delta sigma weight residual 1.331 1.304 0.027 1.48e-02 4.57e+03 3.34e+00 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 100.08 - 108.04: 1282 108.04 - 116.01: 18596 116.01 - 123.97: 20229 123.97 - 131.94: 661 131.94 - 139.91: 45 Bond angle restraints: 40813 Sorted by residual: angle pdb=" C GLU B 347 " pdb=" CA GLU B 347 " pdb=" CB GLU B 347 " ideal model delta sigma weight residual 116.54 110.60 5.94 1.15e+00 7.56e-01 2.67e+01 angle pdb=" N ILE D 470 " pdb=" CA ILE D 470 " pdb=" C ILE D 470 " ideal model delta sigma weight residual 113.53 108.67 4.86 9.80e-01 1.04e+00 2.46e+01 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 109.51 3.69 9.60e-01 1.09e+00 1.48e+01 angle pdb=" C ASN B 442 " pdb=" N VAL B 443 " pdb=" CA VAL B 443 " ideal model delta sigma weight residual 123.16 119.60 3.56 1.06e+00 8.90e-01 1.13e+01 angle pdb=" N GLY C 142 " pdb=" CA GLY C 142 " pdb=" C GLY C 142 " ideal model delta sigma weight residual 114.67 110.09 4.58 1.41e+00 5.03e-01 1.05e+01 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16973 17.98 - 35.97: 1124 35.97 - 53.95: 192 53.95 - 71.94: 63 71.94 - 89.92: 31 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: dihedral pdb=" CA ARG E 372 " pdb=" C ARG E 372 " pdb=" N GLU E 373 " pdb=" CA GLU E 373 " ideal model delta harmonic sigma weight residual -180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA VAL F 21 " pdb=" C VAL F 21 " pdb=" N GLU F 22 " pdb=" CA GLU F 22 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PRO G 120 " pdb=" C PRO G 120 " pdb=" N ALA G 121 " pdb=" CA ALA G 121 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3022 0.034 - 0.068: 1005 0.068 - 0.102: 382 0.102 - 0.136: 155 0.136 - 0.170: 8 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA THR G 119 " pdb=" N THR G 119 " pdb=" C THR G 119 " pdb=" CB THR G 119 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO E 324 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 394 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO F 324 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.021 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 39 2.40 - 3.03: 17194 3.03 - 3.65: 43275 3.65 - 4.28: 66123 4.28 - 4.90: 113720 Nonbonded interactions: 240351 Sorted by model distance: nonbonded pdb=" O3B ADP A 601 " pdb=" O2 PO4 A 603 " model vdw 1.776 3.040 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.954 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.959 2.170 nonbonded pdb=" OG SER A 235 " pdb="MG MG A 602 " model vdw 1.980 2.170 nonbonded pdb=" PB ADP A 601 " pdb=" O2 PO4 A 603 " model vdw 2.017 3.400 ... (remaining 240346 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.630 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 74.910 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 0.057 30114 Z= 0.223 Angle : 0.549 8.032 40813 Z= 0.308 Chirality : 0.043 0.170 4572 Planarity : 0.004 0.046 5333 Dihedral : 13.213 89.923 11465 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.14), residues: 3764 helix: 1.91 (0.14), residues: 1545 sheet: 0.42 (0.22), residues: 563 loop : 0.34 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 119 HIS 0.003 0.001 HIS B 418 PHE 0.018 0.001 PHE G 108 TYR 0.012 0.001 TYR G 133 ARG 0.003 0.000 ARG B 95 *********************** 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 569 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 569 time to evaluate : 3.435 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8047 (mt0) cc_final: 0.7757 (mt0) REVERT: A 8 LYS cc_start: 0.8361 (tttm) cc_final: 0.8014 (tttm) REVERT: A 20 LEU cc_start: 0.8005 (tp) cc_final: 0.7798 (tp) REVERT: A 114 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7223 (mm-30) REVERT: A 122 MET cc_start: 0.7194 (mtp) cc_final: 0.6890 (mtp) REVERT: A 124 LYS cc_start: 0.7205 (mtmm) cc_final: 0.6876 (mptt) REVERT: A 130 ARG cc_start: 0.7557 (ttm110) cc_final: 0.6633 (ptp90) REVERT: A 134 VAL cc_start: 0.8467 (m) cc_final: 0.8249 (t) REVERT: A 161 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7835 (mmtt) REVERT: A 209 MET cc_start: 0.7308 (mtp) cc_final: 0.6944 (mtt) REVERT: A 220 MET cc_start: 0.7174 (tpt) cc_final: 0.6452 (tpt) REVERT: A 261 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6585 (mt-10) REVERT: A 391 MET cc_start: 0.8102 (mmt) cc_final: 0.7843 (mmt) REVERT: A 456 GLU cc_start: 0.6347 (mt-10) cc_final: 0.5989 (mt-10) REVERT: A 466 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6419 (mp0) REVERT: A 491 ARG cc_start: 0.6498 (mmt180) cc_final: 0.5353 (mtm110) REVERT: A 493 ASP cc_start: 0.7526 (m-30) cc_final: 0.7296 (m-30) REVERT: A 537 ASP cc_start: 0.6489 (t0) cc_final: 0.5783 (m-30) REVERT: A 540 LEU cc_start: 0.6395 (mt) cc_final: 0.6102 (mt) REVERT: A 546 GLU cc_start: 0.5750 (pp20) cc_final: 0.5545 (tm-30) REVERT: B 29 LYS cc_start: 0.7631 (mtpt) cc_final: 0.7137 (mtmm) REVERT: B 114 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7243 (mp0) REVERT: B 122 MET cc_start: 0.8085 (mtm) cc_final: 0.7795 (mtp) REVERT: B 130 ARG cc_start: 0.6730 (mtm110) cc_final: 0.6103 (mtp85) REVERT: B 176 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6644 (pt0) REVERT: B 183 MET cc_start: 0.8786 (mtt) cc_final: 0.8472 (mtt) REVERT: B 197 ARG cc_start: 0.7797 (ttp-110) cc_final: 0.7584 (ttp80) REVERT: B 220 MET cc_start: 0.7283 (ttp) cc_final: 0.6771 (tpp) REVERT: B 248 ASP cc_start: 0.6899 (m-30) cc_final: 0.6653 (m-30) REVERT: B 401 ARG cc_start: 0.7536 (ttm170) cc_final: 0.7292 (mmm-85) REVERT: B 425 ASN cc_start: 0.7291 (m110) cc_final: 0.7056 (m-40) REVERT: B 460 ARG cc_start: 0.5711 (mtp180) cc_final: 0.5505 (mtp-110) REVERT: B 477 GLN cc_start: 0.4426 (pp30) cc_final: 0.3551 (mm110) REVERT: B 485 GLU cc_start: 0.6052 (mm-30) cc_final: 0.4730 (tp30) REVERT: B 558 GLU cc_start: 0.6376 (tt0) cc_final: 0.5960 (mm-30) REVERT: C 1 MET cc_start: 0.5734 (mpp) cc_final: 0.5108 (tpt) REVERT: C 56 SER cc_start: 0.7734 (m) cc_final: 0.7234 (p) REVERT: C 128 GLU cc_start: 0.6674 (tp30) cc_final: 0.6276 (mm-30) REVERT: C 130 ARG cc_start: 0.6973 (ttp-110) cc_final: 0.6617 (mtm-85) REVERT: C 158 LYS cc_start: 0.8165 (ttpp) cc_final: 0.7613 (ttmt) REVERT: C 209 MET cc_start: 0.7674 (mtp) cc_final: 0.7209 (mtm) REVERT: C 220 MET cc_start: 0.7703 (mmt) cc_final: 0.7447 (mmt) REVERT: C 344 MET cc_start: 0.7739 (ttm) cc_final: 0.7010 (ttt) REVERT: C 410 ASP cc_start: 0.7732 (t0) cc_final: 0.7525 (t70) REVERT: C 416 ARG cc_start: 0.7389 (ptm-80) cc_final: 0.6761 (mmt90) REVERT: C 424 TRP cc_start: 0.7406 (p90) cc_final: 0.6668 (p-90) REVERT: C 456 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6087 (tp30) REVERT: C 459 GLN cc_start: 0.7152 (mt0) cc_final: 0.6812 (mt0) REVERT: C 524 LYS cc_start: 0.6587 (ttmm) cc_final: 0.6226 (tppp) REVERT: C 541 GLN cc_start: 0.6705 (mp-120) cc_final: 0.6268 (mt0) REVERT: C 546 GLU cc_start: 0.7165 (tp30) cc_final: 0.6811 (tp30) REVERT: C 550 ARG cc_start: 0.7158 (mmt180) cc_final: 0.6676 (mmt180) REVERT: C 568 LYS cc_start: 0.6367 (mttt) cc_final: 0.5960 (mtpp) REVERT: D 5 LYS cc_start: 0.5758 (mmtt) cc_final: 0.4855 (tttp) REVERT: D 36 LYS cc_start: 0.7654 (ttpp) cc_final: 0.7430 (ttpt) REVERT: D 62 GLU cc_start: 0.7197 (tp30) cc_final: 0.6155 (pm20) REVERT: D 67 ASP cc_start: 0.6931 (p0) cc_final: 0.6465 (p0) REVERT: D 86 LYS cc_start: 0.7781 (mtmm) cc_final: 0.7544 (mtpp) REVERT: D 206 GLN cc_start: 0.6620 (tp40) cc_final: 0.6378 (mm-40) REVERT: D 269 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6575 (mt-10) REVERT: D 274 ARG cc_start: 0.6943 (mtt180) cc_final: 0.6732 (mtt180) REVERT: D 302 GLU cc_start: 0.7443 (tt0) cc_final: 0.7117 (tt0) REVERT: D 410 ARG cc_start: 0.6638 (ttm170) cc_final: 0.6339 (mtt180) REVERT: D 413 GLN cc_start: 0.6555 (mt0) cc_final: 0.6304 (mp10) REVERT: D 456 LYS cc_start: 0.6977 (tppt) cc_final: 0.6606 (mmtm) REVERT: D 461 LYS cc_start: 0.7011 (tttm) cc_final: 0.6530 (ttpt) REVERT: E 6 LYS cc_start: 0.7077 (tttt) cc_final: 0.6754 (tttm) REVERT: E 25 LYS cc_start: 0.7637 (mtmm) cc_final: 0.6994 (mppt) REVERT: E 96 ILE cc_start: 0.7760 (tp) cc_final: 0.7546 (tt) REVERT: E 210 ARG cc_start: 0.7516 (ttp80) cc_final: 0.7141 (ttp-170) REVERT: E 290 ASP cc_start: 0.7767 (t70) cc_final: 0.7468 (t70) REVERT: E 368 LYS cc_start: 0.7376 (mtpt) cc_final: 0.7063 (mptt) REVERT: E 380 ASP cc_start: 0.6780 (m-30) cc_final: 0.6179 (m-30) REVERT: E 409 ARG cc_start: 0.6522 (ttm-80) cc_final: 0.6126 (mtm110) REVERT: E 437 GLN cc_start: 0.7488 (tt0) cc_final: 0.7256 (tt0) REVERT: F 7 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6337 (mm-30) REVERT: F 36 LYS cc_start: 0.7411 (ttpt) cc_final: 0.6916 (ttmt) REVERT: F 54 TYR cc_start: 0.8075 (p90) cc_final: 0.7752 (p90) REVERT: F 81 ARG cc_start: 0.7600 (mtt-85) cc_final: 0.7317 (mtt90) REVERT: F 96 ILE cc_start: 0.7769 (pt) cc_final: 0.7416 (pt) REVERT: F 162 GLU cc_start: 0.7095 (mp0) cc_final: 0.6867 (mt-10) REVERT: F 200 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6406 (mt-10) REVERT: F 206 GLN cc_start: 0.6575 (mt0) cc_final: 0.6185 (mp10) REVERT: F 280 ARG cc_start: 0.7666 (mtt180) cc_final: 0.6512 (mtm110) REVERT: F 302 GLU cc_start: 0.7658 (tt0) cc_final: 0.7448 (tt0) REVERT: F 305 LYS cc_start: 0.7268 (mmtm) cc_final: 0.6887 (mtmt) REVERT: F 318 ASP cc_start: 0.6578 (t0) cc_final: 0.6275 (t70) REVERT: F 401 GLU cc_start: 0.6252 (tt0) cc_final: 0.5738 (tp30) REVERT: F 455 SER cc_start: 0.7693 (t) cc_final: 0.7352 (p) REVERT: F 461 LYS cc_start: 0.7339 (tttp) cc_final: 0.7102 (ttmm) REVERT: F 466 LYS cc_start: 0.6875 (mtmm) cc_final: 0.6161 (ttmm) REVERT: G 14 ARG cc_start: 0.6436 (mmp-170) cc_final: 0.5872 (mmt180) REVERT: G 39 PHE cc_start: 0.5382 (t80) cc_final: 0.5151 (t80) REVERT: G 144 GLU cc_start: 0.4629 (tm-30) cc_final: 0.4404 (tt0) REVERT: G 153 GLU cc_start: 0.4755 (mm-30) cc_final: 0.4472 (tp30) REVERT: G 155 LYS cc_start: 0.6043 (mttt) cc_final: 0.5809 (ttpt) REVERT: G 185 GLN cc_start: 0.6093 (tp40) cc_final: 0.5594 (tp40) REVERT: J 88 ARG cc_start: 0.4232 (ppt170) cc_final: 0.3989 (ttp-170) REVERT: J 99 GLU cc_start: 0.2831 (mp0) cc_final: 0.1629 (tp30) REVERT: J 161 THR cc_start: 0.7016 (p) cc_final: 0.6556 (p) REVERT: L 72 ARG cc_start: 0.5326 (ttp-170) cc_final: 0.5089 (ttt-90) REVERT: L 128 LEU cc_start: 0.4664 (pp) cc_final: 0.4000 (mt) outliers start: 0 outliers final: 0 residues processed: 569 average time/residue: 0.5273 time to fit residues: 436.6701 Evaluate side-chains 391 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 3.231 ------------------------------------------------------------------------------- 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: 20.0000 chunk 282 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 338 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 260 ASN B 316 GLN D 170 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 23 ASN F 222 ASN F 323 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30114 Z= 0.393 Angle : 0.677 11.046 40813 Z= 0.348 Chirality : 0.049 0.225 4572 Planarity : 0.006 0.055 5333 Dihedral : 6.539 80.058 4259 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.46 % Allowed : 6.71 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3764 helix: 1.12 (0.13), residues: 1551 sheet: 0.27 (0.22), residues: 565 loop : -0.09 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 119 HIS 0.010 0.002 HIS B 283 PHE 0.023 0.003 PHE C 230 TYR 0.019 0.002 TYR D 463 ARG 0.006 0.001 ARG G 32 *********************** 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 423 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 378 time to evaluate : 3.303 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6114 (mmt) cc_final: 0.4199 (ptp) REVERT: A 3 GLN cc_start: 0.8068 (mt0) cc_final: 0.7767 (mt0) REVERT: A 8 LYS cc_start: 0.8339 (tttm) cc_final: 0.7994 (tttm) REVERT: A 20 LEU cc_start: 0.8113 (tp) cc_final: 0.7835 (tp) REVERT: A 114 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 124 LYS cc_start: 0.7325 (mtmm) cc_final: 0.6879 (mmtp) REVERT: A 134 VAL cc_start: 0.8552 (m) cc_final: 0.8259 (t) REVERT: A 209 MET cc_start: 0.7339 (mtp) cc_final: 0.7122 (mtp) REVERT: A 393 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6598 (pp20) REVERT: A 456 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6010 (tt0) REVERT: A 491 ARG cc_start: 0.6534 (mmt180) cc_final: 0.5415 (mtm110) REVERT: A 493 ASP cc_start: 0.7527 (m-30) cc_final: 0.7306 (m-30) REVERT: A 537 ASP cc_start: 0.6567 (t0) cc_final: 0.6059 (m-30) REVERT: A 540 LEU cc_start: 0.6510 (mt) cc_final: 0.6306 (mt) REVERT: A 546 GLU cc_start: 0.5826 (pp20) cc_final: 0.5471 (tm-30) REVERT: A 557 GLU cc_start: 0.6991 (pp20) cc_final: 0.6207 (mp0) REVERT: B 29 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7204 (mtmm) REVERT: B 130 ARG cc_start: 0.6768 (mtm110) cc_final: 0.6000 (mtp85) REVERT: B 176 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6961 (mm-30) REVERT: B 197 ARG cc_start: 0.7911 (ttp-110) cc_final: 0.7655 (ttp80) REVERT: B 248 ASP cc_start: 0.7073 (m-30) cc_final: 0.6796 (m-30) REVERT: B 323 MET cc_start: 0.8707 (mtt) cc_final: 0.8506 (mtt) REVERT: B 329 ARG cc_start: 0.6647 (mmt-90) cc_final: 0.6289 (mmp80) REVERT: B 341 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7029 (mp) REVERT: B 477 GLN cc_start: 0.4632 (pp30) cc_final: 0.3527 (mm-40) REVERT: B 485 GLU cc_start: 0.6093 (mm-30) cc_final: 0.4760 (tp30) REVERT: B 558 GLU cc_start: 0.6280 (tt0) cc_final: 0.5905 (mt-10) REVERT: C 1 MET cc_start: 0.6168 (mpp) cc_final: 0.5513 (mmm) REVERT: C 128 GLU cc_start: 0.6591 (tp30) cc_final: 0.6187 (mm-30) REVERT: C 130 ARG cc_start: 0.7084 (ttp-110) cc_final: 0.6752 (mtm-85) REVERT: C 424 TRP cc_start: 0.7479 (p90) cc_final: 0.6706 (p-90) REVERT: C 456 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6219 (tp30) REVERT: C 459 GLN cc_start: 0.7332 (mt0) cc_final: 0.6988 (mt0) REVERT: C 476 LEU cc_start: 0.6545 (mp) cc_final: 0.6246 (mt) REVERT: C 541 GLN cc_start: 0.6599 (mp-120) cc_final: 0.6363 (mt0) REVERT: C 546 GLU cc_start: 0.7016 (tp30) cc_final: 0.6662 (tp30) REVERT: C 550 ARG cc_start: 0.7051 (mmt180) cc_final: 0.6556 (mmt180) REVERT: C 569 GLU cc_start: 0.6511 (tt0) cc_final: 0.5989 (mt-10) REVERT: D 67 ASP cc_start: 0.7197 (p0) cc_final: 0.6660 (p0) REVERT: D 86 LYS cc_start: 0.7778 (mtmm) cc_final: 0.7504 (mtpt) REVERT: D 206 GLN cc_start: 0.6815 (tp40) cc_final: 0.6015 (pp30) REVERT: D 394 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.6417 (tttm) REVERT: D 410 ARG cc_start: 0.6598 (ttm170) cc_final: 0.6190 (mtt180) REVERT: D 461 LYS cc_start: 0.6837 (tttm) cc_final: 0.6288 (ttpt) REVERT: E 6 LYS cc_start: 0.7287 (tttt) cc_final: 0.7042 (tttm) REVERT: E 25 LYS cc_start: 0.7701 (mtmm) cc_final: 0.6988 (mppt) REVERT: E 290 ASP cc_start: 0.7135 (t70) cc_final: 0.6870 (t70) REVERT: E 380 ASP cc_start: 0.6950 (m-30) cc_final: 0.6387 (m-30) REVERT: E 407 ASN cc_start: 0.5661 (OUTLIER) cc_final: 0.5265 (t0) REVERT: E 437 GLN cc_start: 0.7631 (tt0) cc_final: 0.7362 (tt0) REVERT: F 7 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6351 (mm-30) REVERT: F 36 LYS cc_start: 0.7435 (ttpt) cc_final: 0.6898 (ttmt) REVERT: F 96 ILE cc_start: 0.7785 (pt) cc_final: 0.7414 (pt) REVERT: F 206 GLN cc_start: 0.6637 (mt0) cc_final: 0.6149 (mp10) REVERT: F 280 ARG cc_start: 0.7759 (mtt180) cc_final: 0.6524 (mtm110) REVERT: F 302 GLU cc_start: 0.7622 (tt0) cc_final: 0.7362 (tt0) REVERT: F 305 LYS cc_start: 0.7176 (mmtm) cc_final: 0.6769 (mtmt) REVERT: F 318 ASP cc_start: 0.6678 (t0) cc_final: 0.6477 (t70) REVERT: F 409 ARG cc_start: 0.6739 (ttm-80) cc_final: 0.6300 (mtt90) REVERT: F 455 SER cc_start: 0.7707 (t) cc_final: 0.7163 (p) REVERT: F 461 LYS cc_start: 0.7209 (tttp) cc_final: 0.6926 (ttmm) REVERT: G 14 ARG cc_start: 0.6544 (mmp-170) cc_final: 0.5856 (mmt180) REVERT: G 23 LYS cc_start: 0.6158 (mtpp) cc_final: 0.5549 (mmmt) REVERT: G 39 PHE cc_start: 0.5400 (t80) cc_final: 0.5149 (t80) REVERT: G 153 GLU cc_start: 0.4697 (mm-30) cc_final: 0.4456 (tp30) REVERT: G 155 LYS cc_start: 0.6125 (mttt) cc_final: 0.5817 (ttpt) REVERT: G 185 GLN cc_start: 0.6233 (tp40) cc_final: 0.5712 (tp40) REVERT: J 85 ARG cc_start: 0.4537 (mtp180) cc_final: 0.4291 (ptp-170) REVERT: L 78 GLU cc_start: 0.5685 (mt-10) cc_final: 0.5434 (tt0) REVERT: L 121 LEU cc_start: 0.6409 (tp) cc_final: 0.5820 (mp) REVERT: L 142 LEU cc_start: 0.5006 (pt) cc_final: 0.4711 (mt) outliers start: 45 outliers final: 31 residues processed: 405 average time/residue: 0.5183 time to fit residues: 308.4860 Evaluate side-chains 375 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 340 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 167 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 281 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 339 optimal weight: 5.9990 chunk 366 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 336 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30114 Z= 0.291 Angle : 0.578 10.827 40813 Z= 0.299 Chirality : 0.046 0.181 4572 Planarity : 0.005 0.050 5333 Dihedral : 6.357 82.308 4259 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.88 % Allowed : 8.92 % Favored : 89.20 % 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: 0.55 (0.14), residues: 3764 helix: 1.07 (0.13), residues: 1552 sheet: 0.23 (0.22), residues: 574 loop : -0.16 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 119 HIS 0.010 0.001 HIS B 283 PHE 0.019 0.002 PHE C 415 TYR 0.014 0.002 TYR D 463 ARG 0.009 0.000 ARG E 321 *********************** 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 407 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 349 time to evaluate : 3.351 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6105 (mmt) cc_final: 0.4170 (ptp) REVERT: A 3 GLN cc_start: 0.8125 (mt0) cc_final: 0.7817 (mt0) REVERT: A 8 LYS cc_start: 0.8333 (tttm) cc_final: 0.7984 (tttm) REVERT: A 20 LEU cc_start: 0.8115 (tp) cc_final: 0.7887 (tp) REVERT: A 114 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7222 (mm-30) REVERT: A 124 LYS cc_start: 0.7291 (mtmm) cc_final: 0.6785 (mmtp) REVERT: A 209 MET cc_start: 0.7405 (mtp) cc_final: 0.7142 (mtp) REVERT: A 393 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6533 (pp20) REVERT: A 456 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6040 (mt-10) REVERT: A 491 ARG cc_start: 0.6548 (mmt180) cc_final: 0.5730 (ttp-110) REVERT: A 493 ASP cc_start: 0.7492 (m-30) cc_final: 0.7264 (m-30) REVERT: A 537 ASP cc_start: 0.6634 (t0) cc_final: 0.6092 (m-30) REVERT: A 546 GLU cc_start: 0.5822 (pp20) cc_final: 0.5471 (tm-30) REVERT: A 557 GLU cc_start: 0.7018 (pp20) cc_final: 0.6226 (mp0) REVERT: B 29 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7163 (mtmm) REVERT: B 48 PHE cc_start: 0.7952 (m-80) cc_final: 0.7422 (m-80) REVERT: B 122 MET cc_start: 0.7983 (mtm) cc_final: 0.7522 (mtp) REVERT: B 130 ARG cc_start: 0.6822 (mtm110) cc_final: 0.6187 (mtp85) REVERT: B 147 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7978 (mp) REVERT: B 176 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6942 (mm-30) REVERT: B 197 ARG cc_start: 0.7931 (ttp-110) cc_final: 0.7709 (ttp80) REVERT: B 248 ASP cc_start: 0.7055 (m-30) cc_final: 0.6754 (m-30) REVERT: B 329 ARG cc_start: 0.6546 (mmt-90) cc_final: 0.6195 (mmp80) REVERT: B 401 ARG cc_start: 0.7512 (ttm170) cc_final: 0.7312 (mtm-85) REVERT: B 409 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6469 (tp) REVERT: B 465 GLN cc_start: 0.5096 (mm-40) cc_final: 0.4424 (mm-40) REVERT: B 477 GLN cc_start: 0.4543 (pp30) cc_final: 0.3350 (mm-40) REVERT: B 481 ARG cc_start: 0.5451 (mtp180) cc_final: 0.5127 (mtp-110) REVERT: B 485 GLU cc_start: 0.6023 (mm-30) cc_final: 0.4680 (tp30) REVERT: B 558 GLU cc_start: 0.6346 (tt0) cc_final: 0.5960 (mt-10) REVERT: C 1 MET cc_start: 0.6068 (mpp) cc_final: 0.5486 (mmm) REVERT: C 130 ARG cc_start: 0.7059 (ttp-110) cc_final: 0.6748 (mtm-85) REVERT: C 393 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: C 424 TRP cc_start: 0.7479 (p90) cc_final: 0.6677 (p-90) REVERT: C 456 GLU cc_start: 0.6555 (mm-30) cc_final: 0.6217 (tp30) REVERT: C 459 GLN cc_start: 0.7325 (mt0) cc_final: 0.7068 (mt0) REVERT: C 476 LEU cc_start: 0.6444 (mp) cc_final: 0.6158 (mt) REVERT: C 541 GLN cc_start: 0.6637 (mp-120) cc_final: 0.6392 (mt0) REVERT: C 546 GLU cc_start: 0.6914 (tp30) cc_final: 0.6590 (tp30) REVERT: C 550 ARG cc_start: 0.7098 (mmt180) cc_final: 0.6412 (mtm110) REVERT: D 67 ASP cc_start: 0.7286 (p0) cc_final: 0.6960 (p0) REVERT: D 86 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7539 (mtpt) REVERT: D 206 GLN cc_start: 0.6746 (tp40) cc_final: 0.6238 (mm-40) REVERT: D 445 MET cc_start: 0.7244 (mtm) cc_final: 0.6977 (mtp) REVERT: D 461 LYS cc_start: 0.6785 (tttm) cc_final: 0.6240 (ttpt) REVERT: E 6 LYS cc_start: 0.7356 (tttt) cc_final: 0.7107 (tttm) REVERT: E 290 ASP cc_start: 0.7059 (t70) cc_final: 0.6798 (t70) REVERT: E 380 ASP cc_start: 0.6916 (m-30) cc_final: 0.6319 (m-30) REVERT: E 409 ARG cc_start: 0.6347 (ttm-80) cc_final: 0.5631 (mtt-85) REVERT: E 437 GLN cc_start: 0.7600 (tt0) cc_final: 0.7361 (tt0) REVERT: F 7 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6270 (mm-30) REVERT: F 36 LYS cc_start: 0.7395 (ttpt) cc_final: 0.6882 (ttmt) REVERT: F 96 ILE cc_start: 0.7808 (pt) cc_final: 0.7448 (pt) REVERT: F 206 GLN cc_start: 0.6737 (mt0) cc_final: 0.6258 (mp10) REVERT: F 280 ARG cc_start: 0.7747 (mtt180) cc_final: 0.6475 (mtm110) REVERT: F 302 GLU cc_start: 0.7634 (tt0) cc_final: 0.7383 (tt0) REVERT: F 305 LYS cc_start: 0.7105 (mmtm) cc_final: 0.6732 (mtmt) REVERT: F 318 ASP cc_start: 0.6583 (t0) cc_final: 0.6382 (t70) REVERT: F 409 ARG cc_start: 0.6704 (ttm-80) cc_final: 0.6258 (mtt90) REVERT: F 455 SER cc_start: 0.7816 (t) cc_final: 0.7229 (p) REVERT: F 461 LYS cc_start: 0.7266 (tttp) cc_final: 0.6963 (ttmm) REVERT: G 14 ARG cc_start: 0.6509 (mmp-170) cc_final: 0.5845 (mmt180) REVERT: G 155 LYS cc_start: 0.6104 (mttt) cc_final: 0.5829 (ttpt) REVERT: G 177 ARG cc_start: 0.6443 (ttp80) cc_final: 0.5687 (ttp-110) REVERT: G 185 GLN cc_start: 0.6223 (tp40) cc_final: 0.5720 (tp40) REVERT: H 103 LYS cc_start: 0.4412 (tttm) cc_final: 0.3521 (pttp) REVERT: J 145 GLU cc_start: 0.3918 (tm-30) cc_final: 0.3714 (tm-30) REVERT: L 142 LEU cc_start: 0.4959 (pt) cc_final: 0.4678 (mt) outliers start: 58 outliers final: 39 residues processed: 389 average time/residue: 0.5011 time to fit residues: 292.7204 Evaluate side-chains 384 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 341 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 167 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 9.9990 chunk 255 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 0.0050 chunk 227 optimal weight: 4.9990 chunk 340 optimal weight: 10.0000 chunk 360 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 322 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 283 HIS F 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30114 Z= 0.296 Angle : 0.582 11.134 40813 Z= 0.298 Chirality : 0.046 0.194 4572 Planarity : 0.005 0.051 5333 Dihedral : 6.317 83.286 4259 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.37 % Allowed : 10.06 % Favored : 87.58 % 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: 0.43 (0.14), residues: 3764 helix: 0.99 (0.13), residues: 1556 sheet: 0.24 (0.23), residues: 544 loop : -0.27 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 119 HIS 0.009 0.001 HIS B 283 PHE 0.018 0.002 PHE A 230 TYR 0.015 0.002 TYR F 349 ARG 0.005 0.000 ARG F 420 *********************** 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 422 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 349 time to evaluate : 3.512 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6264 (mmt) cc_final: 0.4133 (ptp) REVERT: A 3 GLN cc_start: 0.8123 (mt0) cc_final: 0.7800 (mt0) REVERT: A 8 LYS cc_start: 0.8319 (tttm) cc_final: 0.7958 (tttm) REVERT: A 20 LEU cc_start: 0.8128 (tp) cc_final: 0.7915 (tp) REVERT: A 114 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 124 LYS cc_start: 0.7281 (mtmm) cc_final: 0.6762 (mmtp) REVERT: A 183 MET cc_start: 0.8836 (mtt) cc_final: 0.8190 (mtt) REVERT: A 209 MET cc_start: 0.7430 (mtp) cc_final: 0.7150 (mtp) REVERT: A 393 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6570 (pp20) REVERT: A 456 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6056 (mt-10) REVERT: A 491 ARG cc_start: 0.6532 (mmt180) cc_final: 0.5720 (ttp-110) REVERT: A 493 ASP cc_start: 0.7516 (m-30) cc_final: 0.7283 (m-30) REVERT: A 532 ARG cc_start: 0.5399 (OUTLIER) cc_final: 0.4547 (mtp85) REVERT: A 537 ASP cc_start: 0.6591 (t0) cc_final: 0.6049 (m-30) REVERT: A 546 GLU cc_start: 0.5815 (pp20) cc_final: 0.5475 (tm-30) REVERT: B 29 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7151 (mtmm) REVERT: B 48 PHE cc_start: 0.7993 (m-80) cc_final: 0.7388 (m-80) REVERT: B 122 MET cc_start: 0.7937 (mtm) cc_final: 0.7452 (mtp) REVERT: B 130 ARG cc_start: 0.6633 (mtm110) cc_final: 0.6044 (mtp85) REVERT: B 147 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7933 (mp) REVERT: B 176 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6954 (mm-30) REVERT: B 248 ASP cc_start: 0.7057 (m-30) cc_final: 0.6740 (m-30) REVERT: B 329 ARG cc_start: 0.6599 (mmt-90) cc_final: 0.6257 (mmp80) REVERT: B 401 ARG cc_start: 0.7544 (ttm170) cc_final: 0.7338 (mtm-85) REVERT: B 409 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6460 (tp) REVERT: B 465 GLN cc_start: 0.5093 (mm-40) cc_final: 0.4720 (mm-40) REVERT: B 481 ARG cc_start: 0.5477 (mtp180) cc_final: 0.5275 (mtp-110) REVERT: B 485 GLU cc_start: 0.6039 (mm-30) cc_final: 0.4701 (tp30) REVERT: B 558 GLU cc_start: 0.6379 (tt0) cc_final: 0.5962 (mt-10) REVERT: C 1 MET cc_start: 0.6106 (mpp) cc_final: 0.5448 (mmm) REVERT: C 130 ARG cc_start: 0.7009 (ttp-110) cc_final: 0.6691 (mtm-85) REVERT: C 424 TRP cc_start: 0.7513 (p90) cc_final: 0.6694 (p-90) REVERT: C 456 GLU cc_start: 0.6508 (mm-30) cc_final: 0.5960 (tp30) REVERT: C 459 GLN cc_start: 0.7328 (mt0) cc_final: 0.7035 (mt0) REVERT: C 541 GLN cc_start: 0.6656 (mp-120) cc_final: 0.6405 (mt0) REVERT: C 546 GLU cc_start: 0.6873 (tp30) cc_final: 0.6555 (tp30) REVERT: C 550 ARG cc_start: 0.7136 (mmt180) cc_final: 0.6488 (mtm110) REVERT: D 86 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7559 (mtpt) REVERT: D 206 GLN cc_start: 0.6754 (tp40) cc_final: 0.6245 (mm-40) REVERT: D 461 LYS cc_start: 0.6742 (tttm) cc_final: 0.6203 (ttpt) REVERT: E 6 LYS cc_start: 0.7322 (tttt) cc_final: 0.7102 (tttm) REVERT: E 290 ASP cc_start: 0.7075 (t70) cc_final: 0.6818 (t70) REVERT: E 334 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: E 380 ASP cc_start: 0.6902 (m-30) cc_final: 0.6301 (m-30) REVERT: E 409 ARG cc_start: 0.6337 (ttm-80) cc_final: 0.5932 (mtm110) REVERT: E 437 GLN cc_start: 0.7584 (tt0) cc_final: 0.7363 (tt0) REVERT: E 468 GLU cc_start: 0.3189 (OUTLIER) cc_final: 0.2371 (pp20) REVERT: F 7 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6266 (mm-30) REVERT: F 36 LYS cc_start: 0.7346 (ttpt) cc_final: 0.6843 (ttmt) REVERT: F 96 ILE cc_start: 0.7797 (pt) cc_final: 0.7449 (pt) REVERT: F 206 GLN cc_start: 0.6773 (mt0) cc_final: 0.6257 (mp10) REVERT: F 280 ARG cc_start: 0.7779 (mtt180) cc_final: 0.6461 (mtm110) REVERT: F 302 GLU cc_start: 0.7636 (tt0) cc_final: 0.7403 (tt0) REVERT: F 305 LYS cc_start: 0.7027 (mmtm) cc_final: 0.6799 (mttm) REVERT: F 409 ARG cc_start: 0.6701 (ttm-80) cc_final: 0.6223 (mtt90) REVERT: F 455 SER cc_start: 0.7824 (t) cc_final: 0.7233 (p) REVERT: F 461 LYS cc_start: 0.7107 (tttp) cc_final: 0.6792 (ttmm) REVERT: G 14 ARG cc_start: 0.6528 (mmp-170) cc_final: 0.5859 (mmt180) REVERT: G 155 LYS cc_start: 0.6093 (mttt) cc_final: 0.5785 (ttpt) REVERT: G 160 ARG cc_start: 0.5038 (mmm-85) cc_final: 0.4636 (tpt-90) REVERT: G 177 ARG cc_start: 0.6387 (ttp80) cc_final: 0.6000 (ttp-110) REVERT: G 185 GLN cc_start: 0.6219 (tp40) cc_final: 0.5708 (tp40) REVERT: J 145 GLU cc_start: 0.3927 (tm-30) cc_final: 0.3725 (tm-30) REVERT: L 74 GLN cc_start: 0.5596 (tt0) cc_final: 0.5321 (mt0) REVERT: L 94 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.5044 (mm) REVERT: L 142 LEU cc_start: 0.4905 (pt) cc_final: 0.4656 (mt) outliers start: 73 outliers final: 55 residues processed: 407 average time/residue: 0.4919 time to fit residues: 300.6465 Evaluate side-chains 393 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 331 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain L residue 94 LEU 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: 10.0000 chunk 5 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 307 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 323 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30114 Z= 0.329 Angle : 0.607 11.293 40813 Z= 0.312 Chirality : 0.047 0.210 4572 Planarity : 0.006 0.051 5333 Dihedral : 6.407 84.659 4259 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.85 % Allowed : 11.03 % Favored : 86.12 % 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: 0.29 (0.14), residues: 3764 helix: 0.91 (0.13), residues: 1541 sheet: 0.18 (0.23), residues: 544 loop : -0.38 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 119 HIS 0.010 0.001 HIS B 283 PHE 0.018 0.002 PHE C 230 TYR 0.016 0.002 TYR F 349 ARG 0.006 0.001 ARG H 91 *********************** 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 424 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 336 time to evaluate : 3.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6313 (mmt) cc_final: 0.5877 (mmt) REVERT: A 28 CYS cc_start: 0.8312 (m) cc_final: 0.8065 (m) REVERT: A 55 THR cc_start: 0.8844 (p) cc_final: 0.8623 (p) REVERT: A 114 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7142 (mm-30) REVERT: A 124 LYS cc_start: 0.7275 (mtmm) cc_final: 0.6704 (mmtp) REVERT: A 183 MET cc_start: 0.8873 (mtt) cc_final: 0.8244 (mtt) REVERT: A 209 MET cc_start: 0.7453 (mtp) cc_final: 0.7159 (mtp) REVERT: A 393 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6759 (pp20) REVERT: A 456 GLU cc_start: 0.6468 (mt-10) cc_final: 0.6080 (mt-10) REVERT: A 491 ARG cc_start: 0.6522 (mmt180) cc_final: 0.5716 (ttp-110) REVERT: A 493 ASP cc_start: 0.7481 (m-30) cc_final: 0.7252 (m-30) REVERT: A 532 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.4646 (mtp85) REVERT: A 537 ASP cc_start: 0.6626 (t0) cc_final: 0.6053 (m-30) REVERT: A 546 GLU cc_start: 0.5855 (pp20) cc_final: 0.5500 (tm-30) REVERT: B 48 PHE cc_start: 0.7925 (m-80) cc_final: 0.7308 (m-80) REVERT: B 122 MET cc_start: 0.7921 (mtm) cc_final: 0.7392 (mtp) REVERT: B 130 ARG cc_start: 0.6688 (mtm110) cc_final: 0.6130 (mtp85) REVERT: B 147 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7896 (mp) REVERT: B 154 ARG cc_start: 0.7416 (mtm110) cc_final: 0.6564 (mtt90) REVERT: B 248 ASP cc_start: 0.7078 (m-30) cc_final: 0.6748 (m-30) REVERT: B 329 ARG cc_start: 0.6635 (mmt-90) cc_final: 0.6313 (mmp80) REVERT: B 401 ARG cc_start: 0.7568 (ttm170) cc_final: 0.7361 (mtm-85) REVERT: B 409 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6428 (tp) REVERT: B 465 GLN cc_start: 0.5073 (mm-40) cc_final: 0.4688 (mm-40) REVERT: B 477 GLN cc_start: 0.4501 (pp30) cc_final: 0.3147 (mm-40) REVERT: B 485 GLU cc_start: 0.5997 (mm-30) cc_final: 0.4754 (tp30) REVERT: B 558 GLU cc_start: 0.6388 (tt0) cc_final: 0.5967 (mt-10) REVERT: C 1 MET cc_start: 0.6036 (mpp) cc_final: 0.5552 (mmm) REVERT: C 130 ARG cc_start: 0.7025 (ttp-110) cc_final: 0.6681 (mtm-85) REVERT: C 393 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: C 424 TRP cc_start: 0.7483 (p90) cc_final: 0.6658 (p-90) REVERT: C 456 GLU cc_start: 0.6474 (mm-30) cc_final: 0.5954 (tp30) REVERT: C 459 GLN cc_start: 0.7290 (mt0) cc_final: 0.7067 (mt0) REVERT: C 541 GLN cc_start: 0.6649 (mp-120) cc_final: 0.6394 (mt0) REVERT: C 546 GLU cc_start: 0.6808 (tp30) cc_final: 0.6476 (tp30) REVERT: C 550 ARG cc_start: 0.7146 (mmt180) cc_final: 0.6413 (mtm110) REVERT: D 86 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7482 (mtpt) REVERT: D 206 GLN cc_start: 0.6871 (tp40) cc_final: 0.6347 (mm-40) REVERT: D 461 LYS cc_start: 0.6708 (tttm) cc_final: 0.6158 (ttpt) REVERT: E 6 LYS cc_start: 0.7333 (tttt) cc_final: 0.7117 (tttm) REVERT: E 334 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: E 380 ASP cc_start: 0.6904 (m-30) cc_final: 0.6307 (m-30) REVERT: E 409 ARG cc_start: 0.6283 (ttm-80) cc_final: 0.5894 (mtm110) REVERT: E 468 GLU cc_start: 0.3192 (OUTLIER) cc_final: 0.2373 (pp20) REVERT: F 7 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6181 (mm-30) REVERT: F 36 LYS cc_start: 0.7342 (ttpt) cc_final: 0.6876 (ttmt) REVERT: F 96 ILE cc_start: 0.7787 (pt) cc_final: 0.7450 (pt) REVERT: F 206 GLN cc_start: 0.6774 (mt0) cc_final: 0.6211 (mp10) REVERT: F 280 ARG cc_start: 0.7826 (mtt180) cc_final: 0.6445 (mtm110) REVERT: F 305 LYS cc_start: 0.7052 (mmtm) cc_final: 0.6784 (mttm) REVERT: F 409 ARG cc_start: 0.6678 (ttm-80) cc_final: 0.6150 (mtt90) REVERT: F 455 SER cc_start: 0.7792 (t) cc_final: 0.7182 (p) REVERT: F 461 LYS cc_start: 0.7065 (tttp) cc_final: 0.6737 (ttmm) REVERT: G 148 LYS cc_start: 0.5538 (pttt) cc_final: 0.5024 (mttt) REVERT: G 155 LYS cc_start: 0.6132 (mttt) cc_final: 0.5839 (ttpt) REVERT: G 177 ARG cc_start: 0.6401 (ttp80) cc_final: 0.5601 (ttp-110) REVERT: G 184 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6527 (tt0) REVERT: G 185 GLN cc_start: 0.6201 (tp40) cc_final: 0.5735 (tp40) REVERT: J 145 GLU cc_start: 0.3919 (OUTLIER) cc_final: 0.3709 (tm-30) REVERT: L 74 GLN cc_start: 0.5627 (tt0) cc_final: 0.5305 (mt0) REVERT: L 94 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.5048 (mm) REVERT: L 142 LEU cc_start: 0.4910 (pt) cc_final: 0.4645 (mt) outliers start: 88 outliers final: 65 residues processed: 407 average time/residue: 0.5325 time to fit residues: 330.5991 Evaluate side-chains 399 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 324 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 0.0870 chunk 324 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 360 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 189 optimal weight: 0.5980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 310 GLN G 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30114 Z= 0.130 Angle : 0.484 12.279 40813 Z= 0.247 Chirality : 0.042 0.178 4572 Planarity : 0.004 0.049 5333 Dihedral : 5.837 80.282 4259 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.56 % Allowed : 12.36 % Favored : 86.08 % 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: 0.75 (0.14), residues: 3764 helix: 1.29 (0.14), residues: 1562 sheet: 0.34 (0.22), residues: 564 loop : -0.12 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 330 HIS 0.002 0.000 HIS B 283 PHE 0.014 0.001 PHE A 230 TYR 0.011 0.001 TYR G 133 ARG 0.005 0.000 ARG H 91 *********************** 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 399 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 351 time to evaluate : 3.397 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6251 (mmt) cc_final: 0.5821 (mmt) REVERT: A 55 THR cc_start: 0.8790 (p) cc_final: 0.8555 (p) REVERT: A 114 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7179 (mm-30) REVERT: A 124 LYS cc_start: 0.7237 (mtmm) cc_final: 0.6700 (mmtp) REVERT: A 183 MET cc_start: 0.8884 (mtt) cc_final: 0.8301 (mtt) REVERT: A 209 MET cc_start: 0.7369 (mtp) cc_final: 0.7060 (mtp) REVERT: A 276 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6529 (ptpt) REVERT: A 393 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6639 (pp20) REVERT: A 456 GLU cc_start: 0.6485 (mt-10) cc_final: 0.6098 (mt-10) REVERT: A 491 ARG cc_start: 0.6510 (mmt180) cc_final: 0.5711 (ttp-110) REVERT: A 530 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6653 (mt) REVERT: A 537 ASP cc_start: 0.6580 (t0) cc_final: 0.5990 (m-30) REVERT: A 546 GLU cc_start: 0.5789 (pp20) cc_final: 0.5481 (tm-30) REVERT: B 48 PHE cc_start: 0.7868 (m-80) cc_final: 0.7212 (m-80) REVERT: B 108 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7715 (t) REVERT: B 130 ARG cc_start: 0.6682 (mtm110) cc_final: 0.6145 (mtp85) REVERT: B 154 ARG cc_start: 0.7247 (mtm110) cc_final: 0.6328 (mtt90) REVERT: B 248 ASP cc_start: 0.7023 (m-30) cc_final: 0.6691 (m-30) REVERT: B 329 ARG cc_start: 0.6411 (mmt-90) cc_final: 0.6078 (mmp80) REVERT: B 342 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6970 (mt-10) REVERT: B 465 GLN cc_start: 0.5069 (mm-40) cc_final: 0.4661 (mm-40) REVERT: B 477 GLN cc_start: 0.4643 (pp30) cc_final: 0.3424 (mm-40) REVERT: B 485 GLU cc_start: 0.6014 (mm-30) cc_final: 0.4653 (tm-30) REVERT: B 558 GLU cc_start: 0.6373 (tt0) cc_final: 0.5934 (mt-10) REVERT: C 1 MET cc_start: 0.6053 (mpp) cc_final: 0.5442 (mmm) REVERT: C 130 ARG cc_start: 0.7052 (ttp-110) cc_final: 0.6734 (mtm-85) REVERT: C 209 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7444 (mtm) REVERT: C 393 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: C 424 TRP cc_start: 0.7459 (p90) cc_final: 0.6624 (p-90) REVERT: C 456 GLU cc_start: 0.6480 (mm-30) cc_final: 0.5974 (tp30) REVERT: C 459 GLN cc_start: 0.7253 (mt0) cc_final: 0.7051 (mt0) REVERT: C 541 GLN cc_start: 0.6628 (mp-120) cc_final: 0.6351 (mt0) REVERT: C 546 GLU cc_start: 0.6811 (tp30) cc_final: 0.6451 (tp30) REVERT: C 550 ARG cc_start: 0.7207 (mmt180) cc_final: 0.6519 (mtm110) REVERT: D 5 LYS cc_start: 0.5519 (mmtt) cc_final: 0.4852 (ttpp) REVERT: D 86 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7565 (mtpt) REVERT: D 206 GLN cc_start: 0.6778 (tp40) cc_final: 0.6233 (mm-40) REVERT: D 461 LYS cc_start: 0.6753 (tttm) cc_final: 0.6218 (ttpt) REVERT: E 6 LYS cc_start: 0.7263 (tttt) cc_final: 0.7057 (tttm) REVERT: E 290 ASP cc_start: 0.7024 (t70) cc_final: 0.6756 (t70) REVERT: E 334 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: E 380 ASP cc_start: 0.6797 (m-30) cc_final: 0.6187 (m-30) REVERT: E 409 ARG cc_start: 0.6223 (ttm-80) cc_final: 0.5835 (mtm110) REVERT: E 468 GLU cc_start: 0.3353 (OUTLIER) cc_final: 0.3081 (pm20) REVERT: F 7 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6277 (mm-30) REVERT: F 36 LYS cc_start: 0.7257 (ttpt) cc_final: 0.6800 (ttmt) REVERT: F 206 GLN cc_start: 0.6738 (mt0) cc_final: 0.6191 (mp10) REVERT: F 280 ARG cc_start: 0.7745 (mtt180) cc_final: 0.6376 (mtm110) REVERT: F 305 LYS cc_start: 0.7075 (mmtm) cc_final: 0.6801 (mttm) REVERT: F 445 MET cc_start: 0.8219 (mtt) cc_final: 0.8005 (mtp) REVERT: F 455 SER cc_start: 0.7833 (t) cc_final: 0.7326 (p) REVERT: F 461 LYS cc_start: 0.7074 (tttp) cc_final: 0.6761 (ttmm) REVERT: G 148 LYS cc_start: 0.5578 (pttt) cc_final: 0.5052 (mttt) REVERT: G 177 ARG cc_start: 0.6347 (ttp80) cc_final: 0.5659 (mtm-85) REVERT: G 185 GLN cc_start: 0.6072 (tp40) cc_final: 0.5603 (tp40) REVERT: G 190 ASP cc_start: 0.6866 (m-30) cc_final: 0.6522 (m-30) REVERT: J 143 GLN cc_start: 0.3316 (OUTLIER) cc_final: 0.2228 (tt0) REVERT: L 74 GLN cc_start: 0.5662 (tt0) cc_final: 0.5285 (mt0) REVERT: L 94 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.4977 (mm) REVERT: L 121 LEU cc_start: 0.6223 (tt) cc_final: 0.5815 (mt) REVERT: L 142 LEU cc_start: 0.5027 (pt) cc_final: 0.4699 (mt) outliers start: 48 outliers final: 29 residues processed: 386 average time/residue: 0.4891 time to fit residues: 283.9798 Evaluate side-chains 375 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 336 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 20.0000 chunk 40 optimal weight: 0.0020 chunk 205 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 359 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 overall best weight: 6.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 30114 Z= 0.427 Angle : 0.671 11.861 40813 Z= 0.343 Chirality : 0.049 0.238 4572 Planarity : 0.006 0.063 5333 Dihedral : 6.479 85.268 4259 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.85 % Allowed : 11.97 % Favored : 85.18 % 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: 0.17 (0.14), residues: 3764 helix: 0.82 (0.13), residues: 1549 sheet: 0.11 (0.23), residues: 550 loop : -0.46 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 119 HIS 0.011 0.002 HIS B 283 PHE 0.022 0.002 PHE C 230 TYR 0.021 0.002 TYR E 13 ARG 0.006 0.001 ARG A 532 *********************** 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 409 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 321 time to evaluate : 3.505 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6161 (mmt) cc_final: 0.5765 (mmt) REVERT: A 59 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8087 (mtpt) REVERT: A 114 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7128 (mm-30) REVERT: A 124 LYS cc_start: 0.7324 (mtmm) cc_final: 0.6717 (mmtp) REVERT: A 133 MET cc_start: 0.7550 (mtm) cc_final: 0.7297 (mtp) REVERT: A 183 MET cc_start: 0.8860 (mtt) cc_final: 0.8357 (mtt) REVERT: A 209 MET cc_start: 0.7499 (mtp) cc_final: 0.7191 (mtp) REVERT: A 393 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6705 (pp20) REVERT: A 456 GLU cc_start: 0.6485 (mt-10) cc_final: 0.6093 (mt-10) REVERT: A 491 ARG cc_start: 0.6514 (mmt180) cc_final: 0.5731 (ttp-110) REVERT: A 537 ASP cc_start: 0.6599 (t0) cc_final: 0.6004 (m-30) REVERT: A 542 LEU cc_start: 0.6019 (mt) cc_final: 0.5773 (mt) REVERT: A 546 GLU cc_start: 0.5827 (pp20) cc_final: 0.5477 (tm-30) REVERT: B 48 PHE cc_start: 0.7898 (m-80) cc_final: 0.7290 (m-80) REVERT: B 130 ARG cc_start: 0.6663 (mtm110) cc_final: 0.6161 (mtp85) REVERT: B 154 ARG cc_start: 0.7444 (mtm110) cc_final: 0.6584 (mtt90) REVERT: B 248 ASP cc_start: 0.7148 (m-30) cc_final: 0.6807 (m-30) REVERT: B 329 ARG cc_start: 0.6689 (mmt-90) cc_final: 0.6369 (mmp80) REVERT: B 409 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6469 (tp) REVERT: B 465 GLN cc_start: 0.5136 (mm-40) cc_final: 0.4708 (mm-40) REVERT: B 477 GLN cc_start: 0.4518 (pp30) cc_final: 0.3154 (mm-40) REVERT: B 485 GLU cc_start: 0.6067 (mm-30) cc_final: 0.4879 (tp30) REVERT: B 558 GLU cc_start: 0.6408 (tt0) cc_final: 0.6000 (mt-10) REVERT: C 1 MET cc_start: 0.6114 (mpp) cc_final: 0.5638 (mmm) REVERT: C 130 ARG cc_start: 0.7067 (ttp-110) cc_final: 0.6723 (mtm-85) REVERT: C 209 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7342 (mtm) REVERT: C 393 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7148 (tt0) REVERT: C 424 TRP cc_start: 0.7449 (p90) cc_final: 0.6639 (p-90) REVERT: C 459 GLN cc_start: 0.7319 (mt0) cc_final: 0.7019 (mt0) REVERT: C 541 GLN cc_start: 0.6734 (mp-120) cc_final: 0.6460 (mt0) REVERT: C 546 GLU cc_start: 0.6806 (tp30) cc_final: 0.6475 (tp30) REVERT: C 550 ARG cc_start: 0.7113 (mmt180) cc_final: 0.6421 (mtm110) REVERT: D 5 LYS cc_start: 0.5580 (mmtt) cc_final: 0.4894 (ttpp) REVERT: D 86 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7519 (mtpt) REVERT: D 206 GLN cc_start: 0.6843 (tp40) cc_final: 0.6346 (mm-40) REVERT: D 461 LYS cc_start: 0.6703 (tttm) cc_final: 0.6154 (ttpt) REVERT: E 6 LYS cc_start: 0.7376 (tttt) cc_final: 0.7166 (tttm) REVERT: E 334 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: E 380 ASP cc_start: 0.6944 (m-30) cc_final: 0.6315 (m-30) REVERT: E 409 ARG cc_start: 0.6288 (ttm-80) cc_final: 0.5886 (mtm110) REVERT: E 468 GLU cc_start: 0.3118 (OUTLIER) cc_final: 0.2430 (pp20) REVERT: F 7 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6214 (mm-30) REVERT: F 96 ILE cc_start: 0.7692 (pt) cc_final: 0.7362 (tp) REVERT: F 280 ARG cc_start: 0.7831 (mtt180) cc_final: 0.6427 (mtm110) REVERT: F 305 LYS cc_start: 0.6977 (mmtm) cc_final: 0.6723 (mttm) REVERT: F 455 SER cc_start: 0.7817 (t) cc_final: 0.7173 (p) REVERT: F 461 LYS cc_start: 0.7001 (tttp) cc_final: 0.6692 (ttmm) REVERT: G 148 LYS cc_start: 0.5631 (pttt) cc_final: 0.5123 (mttt) REVERT: G 160 ARG cc_start: 0.5678 (mmm-85) cc_final: 0.5272 (tpt-90) REVERT: G 177 ARG cc_start: 0.6432 (ttp80) cc_final: 0.5598 (ttp-110) REVERT: G 185 GLN cc_start: 0.6228 (tp40) cc_final: 0.5771 (tp40) REVERT: H 93 LEU cc_start: 0.4920 (mt) cc_final: 0.4680 (mp) REVERT: J 143 GLN cc_start: 0.3228 (OUTLIER) cc_final: 0.2161 (tt0) REVERT: L 74 GLN cc_start: 0.5620 (tt0) cc_final: 0.5272 (mt0) REVERT: L 94 LEU cc_start: 0.5434 (OUTLIER) cc_final: 0.5074 (mm) REVERT: L 142 LEU cc_start: 0.4844 (pt) cc_final: 0.4615 (mt) outliers start: 88 outliers final: 67 residues processed: 390 average time/residue: 0.4870 time to fit residues: 287.4838 Evaluate side-chains 390 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 315 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 228 optimal weight: 0.0170 chunk 244 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30114 Z= 0.145 Angle : 0.495 11.527 40813 Z= 0.254 Chirality : 0.042 0.172 4572 Planarity : 0.005 0.050 5333 Dihedral : 5.906 82.448 4259 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.75 % Allowed : 12.97 % Favored : 85.27 % 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: 0.62 (0.14), residues: 3764 helix: 1.20 (0.14), residues: 1567 sheet: 0.35 (0.23), residues: 550 loop : -0.24 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 471 HIS 0.004 0.001 HIS B 283 PHE 0.013 0.001 PHE A 230 TYR 0.018 0.001 TYR E 13 ARG 0.008 0.000 ARG A 130 *********************** 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 381 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 327 time to evaluate : 3.616 Fit side-chains REVERT: A 1 MET cc_start: 0.6235 (mmt) cc_final: 0.5832 (mpp) REVERT: A 55 THR cc_start: 0.8819 (p) cc_final: 0.8599 (p) REVERT: A 114 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 124 LYS cc_start: 0.7275 (mtmm) cc_final: 0.6701 (mmtp) REVERT: A 183 MET cc_start: 0.8871 (mtt) cc_final: 0.8249 (mtt) REVERT: A 209 MET cc_start: 0.7403 (mtp) cc_final: 0.7103 (mtp) REVERT: A 276 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6548 (ptpt) REVERT: A 393 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6669 (pp20) REVERT: A 456 GLU cc_start: 0.6517 (mt-10) cc_final: 0.6151 (mt-10) REVERT: A 491 ARG cc_start: 0.6491 (mmt180) cc_final: 0.5696 (ttp-110) REVERT: A 530 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6642 (mt) REVERT: A 537 ASP cc_start: 0.6593 (t0) cc_final: 0.5992 (m-30) REVERT: A 542 LEU cc_start: 0.5971 (mt) cc_final: 0.5705 (mt) REVERT: A 546 GLU cc_start: 0.5843 (pp20) cc_final: 0.5507 (tm-30) REVERT: B 108 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7694 (t) REVERT: B 130 ARG cc_start: 0.6686 (mtm110) cc_final: 0.6174 (mtp85) REVERT: B 154 ARG cc_start: 0.7269 (mtm110) cc_final: 0.6353 (mtt90) REVERT: B 220 MET cc_start: 0.7235 (ttp) cc_final: 0.6834 (tpp) REVERT: B 248 ASP cc_start: 0.7038 (m-30) cc_final: 0.6688 (m-30) REVERT: B 329 ARG cc_start: 0.6431 (mmt-90) cc_final: 0.6124 (mmp80) REVERT: B 342 GLU cc_start: 0.7255 (mt-10) cc_final: 0.7010 (mt-10) REVERT: B 409 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6440 (tp) REVERT: B 465 GLN cc_start: 0.5075 (mm-40) cc_final: 0.4660 (mm-40) REVERT: B 477 GLN cc_start: 0.4551 (pp30) cc_final: 0.3338 (mm-40) REVERT: B 485 GLU cc_start: 0.6037 (mm-30) cc_final: 0.4681 (tm-30) REVERT: B 558 GLU cc_start: 0.6414 (tt0) cc_final: 0.5956 (mt-10) REVERT: C 1 MET cc_start: 0.6064 (mpp) cc_final: 0.5498 (mmm) REVERT: C 130 ARG cc_start: 0.7034 (ttp-110) cc_final: 0.6719 (mtm-85) REVERT: C 156 ARG cc_start: 0.7486 (mtp180) cc_final: 0.7159 (mmm-85) REVERT: C 180 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7243 (mm-30) REVERT: C 209 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7445 (mtm) REVERT: C 393 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: C 424 TRP cc_start: 0.7471 (p90) cc_final: 0.6608 (p-90) REVERT: C 459 GLN cc_start: 0.7254 (mt0) cc_final: 0.7049 (mt0) REVERT: C 541 GLN cc_start: 0.6632 (mp-120) cc_final: 0.6371 (mt0) REVERT: C 546 GLU cc_start: 0.6875 (tp30) cc_final: 0.6521 (tp30) REVERT: C 550 ARG cc_start: 0.7166 (mmt180) cc_final: 0.6490 (mtm110) REVERT: D 5 LYS cc_start: 0.5495 (mmtt) cc_final: 0.4980 (tptt) REVERT: D 34 ASP cc_start: 0.7245 (m-30) cc_final: 0.7002 (m-30) REVERT: D 206 GLN cc_start: 0.6811 (tp40) cc_final: 0.6253 (mm-40) REVERT: D 410 ARG cc_start: 0.6213 (mtp180) cc_final: 0.5946 (mtp180) REVERT: D 461 LYS cc_start: 0.6732 (tttm) cc_final: 0.6183 (ttpt) REVERT: E 290 ASP cc_start: 0.7044 (t70) cc_final: 0.6775 (t70) REVERT: E 334 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: E 380 ASP cc_start: 0.6828 (m-30) cc_final: 0.6226 (m-30) REVERT: E 409 ARG cc_start: 0.6259 (ttm-80) cc_final: 0.5878 (mtm110) REVERT: E 468 GLU cc_start: 0.3364 (OUTLIER) cc_final: 0.3094 (pm20) REVERT: F 7 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6272 (mm-30) REVERT: F 96 ILE cc_start: 0.7734 (pt) cc_final: 0.7413 (tp) REVERT: F 206 GLN cc_start: 0.6624 (mt0) cc_final: 0.6100 (mp10) REVERT: F 280 ARG cc_start: 0.7742 (mtt180) cc_final: 0.6359 (mtm110) REVERT: F 305 LYS cc_start: 0.7029 (mmtm) cc_final: 0.6770 (mttm) REVERT: F 455 SER cc_start: 0.7857 (t) cc_final: 0.7325 (p) REVERT: F 461 LYS cc_start: 0.7069 (tttp) cc_final: 0.6749 (ttmm) REVERT: G 14 ARG cc_start: 0.6516 (mmp-170) cc_final: 0.5836 (mmt180) REVERT: G 148 LYS cc_start: 0.5537 (pttt) cc_final: 0.5058 (mttt) REVERT: G 177 ARG cc_start: 0.6302 (ttp80) cc_final: 0.5600 (mtm-85) REVERT: G 185 GLN cc_start: 0.6126 (tp40) cc_final: 0.5640 (tp40) REVERT: G 190 ASP cc_start: 0.6917 (m-30) cc_final: 0.6570 (m-30) REVERT: H 93 LEU cc_start: 0.4652 (mt) cc_final: 0.4385 (mp) REVERT: J 143 GLN cc_start: 0.3387 (OUTLIER) cc_final: 0.2269 (tt0) REVERT: L 74 GLN cc_start: 0.5714 (tt0) cc_final: 0.5320 (mt0) REVERT: L 94 LEU cc_start: 0.5364 (OUTLIER) cc_final: 0.4975 (mm) REVERT: L 121 LEU cc_start: 0.6167 (tt) cc_final: 0.5801 (mp) REVERT: L 142 LEU cc_start: 0.5087 (pt) cc_final: 0.4711 (mt) outliers start: 54 outliers final: 40 residues processed: 367 average time/residue: 0.4936 time to fit residues: 275.0019 Evaluate side-chains 372 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 321 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 6.9990 chunk 344 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 335 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 316 optimal weight: 20.0000 chunk 333 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 30114 Z= 0.428 Angle : 0.657 12.573 40813 Z= 0.337 Chirality : 0.049 0.232 4572 Planarity : 0.006 0.057 5333 Dihedral : 6.431 85.689 4259 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.47 % Allowed : 12.59 % Favored : 84.95 % 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: 0.16 (0.14), residues: 3764 helix: 0.83 (0.13), residues: 1549 sheet: 0.12 (0.23), residues: 547 loop : -0.49 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 119 HIS 0.010 0.002 HIS B 283 PHE 0.021 0.002 PHE C 230 TYR 0.021 0.002 TYR E 13 ARG 0.007 0.001 ARG A 130 *********************** 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 393 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 317 time to evaluate : 3.384 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6244 (mmt) cc_final: 0.5601 (mmm) REVERT: A 59 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8080 (mtpt) REVERT: A 114 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6968 (mm-30) REVERT: A 124 LYS cc_start: 0.7252 (mtmm) cc_final: 0.6709 (mmtp) REVERT: A 183 MET cc_start: 0.8860 (mtt) cc_final: 0.8249 (mtt) REVERT: A 209 MET cc_start: 0.7461 (mtp) cc_final: 0.7141 (mtp) REVERT: A 393 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6633 (pp20) REVERT: A 456 GLU cc_start: 0.6468 (mt-10) cc_final: 0.6079 (mt-10) REVERT: A 491 ARG cc_start: 0.6502 (mmt180) cc_final: 0.5689 (ttp-110) REVERT: A 537 ASP cc_start: 0.6568 (t0) cc_final: 0.5956 (m-30) REVERT: A 542 LEU cc_start: 0.6028 (mt) cc_final: 0.5777 (mt) REVERT: A 546 GLU cc_start: 0.5869 (pp20) cc_final: 0.5503 (tm-30) REVERT: B 130 ARG cc_start: 0.6675 (mtm110) cc_final: 0.6183 (mtp85) REVERT: B 154 ARG cc_start: 0.7434 (mtm110) cc_final: 0.6577 (mtt90) REVERT: B 248 ASP cc_start: 0.7184 (m-30) cc_final: 0.6834 (m-30) REVERT: B 329 ARG cc_start: 0.6697 (mmt-90) cc_final: 0.6380 (mmp80) REVERT: B 409 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6459 (tp) REVERT: B 465 GLN cc_start: 0.5234 (mm-40) cc_final: 0.4807 (mm-40) REVERT: B 477 GLN cc_start: 0.4546 (pp30) cc_final: 0.3168 (mm-40) REVERT: B 485 GLU cc_start: 0.6073 (mm-30) cc_final: 0.4894 (tp30) REVERT: B 558 GLU cc_start: 0.6411 (tt0) cc_final: 0.6009 (mt-10) REVERT: C 1 MET cc_start: 0.6116 (mpp) cc_final: 0.5626 (mmm) REVERT: C 130 ARG cc_start: 0.7104 (ttp-110) cc_final: 0.6697 (mtm-85) REVERT: C 209 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7332 (mtm) REVERT: C 393 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: C 424 TRP cc_start: 0.7454 (p90) cc_final: 0.6644 (p-90) REVERT: C 459 GLN cc_start: 0.7311 (mt0) cc_final: 0.6996 (mt0) REVERT: C 541 GLN cc_start: 0.6756 (mp-120) cc_final: 0.6472 (mt0) REVERT: C 546 GLU cc_start: 0.6773 (tp30) cc_final: 0.6459 (tp30) REVERT: C 550 ARG cc_start: 0.7095 (mmt180) cc_final: 0.6423 (mtm110) REVERT: D 5 LYS cc_start: 0.5580 (mmtt) cc_final: 0.4896 (ttpp) REVERT: D 206 GLN cc_start: 0.6836 (tp40) cc_final: 0.6340 (mm-40) REVERT: D 410 ARG cc_start: 0.6278 (mtp180) cc_final: 0.6013 (mtp180) REVERT: D 461 LYS cc_start: 0.6692 (tttm) cc_final: 0.6141 (ttpt) REVERT: E 185 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6020 (pt0) REVERT: E 334 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: E 380 ASP cc_start: 0.6945 (m-30) cc_final: 0.6319 (m-30) REVERT: E 409 ARG cc_start: 0.6276 (ttm-80) cc_final: 0.5863 (mtm110) REVERT: E 468 GLU cc_start: 0.3204 (OUTLIER) cc_final: 0.2444 (pp20) REVERT: F 7 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6215 (mm-30) REVERT: F 96 ILE cc_start: 0.7711 (pt) cc_final: 0.7377 (tp) REVERT: F 162 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: F 280 ARG cc_start: 0.7822 (mtt180) cc_final: 0.6456 (mtm110) REVERT: F 305 LYS cc_start: 0.6953 (mmtm) cc_final: 0.6706 (mttm) REVERT: F 455 SER cc_start: 0.7819 (t) cc_final: 0.7178 (p) REVERT: F 461 LYS cc_start: 0.7005 (tttp) cc_final: 0.6692 (ttmm) REVERT: G 14 ARG cc_start: 0.6629 (mmp-170) cc_final: 0.5949 (mmt180) REVERT: G 148 LYS cc_start: 0.5698 (pttt) cc_final: 0.5176 (mttt) REVERT: G 177 ARG cc_start: 0.6431 (ttp80) cc_final: 0.5595 (ttp-110) REVERT: G 185 GLN cc_start: 0.6224 (tp40) cc_final: 0.5760 (tp40) REVERT: H 93 LEU cc_start: 0.4789 (mt) cc_final: 0.4505 (mp) REVERT: J 143 GLN cc_start: 0.3332 (OUTLIER) cc_final: 0.2249 (tt0) REVERT: L 74 GLN cc_start: 0.5656 (tt0) cc_final: 0.5302 (mt0) REVERT: L 94 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.5030 (mm) REVERT: L 121 LEU cc_start: 0.5967 (tt) cc_final: 0.5567 (mp) REVERT: L 142 LEU cc_start: 0.4997 (pt) cc_final: 0.4631 (mt) outliers start: 76 outliers final: 62 residues processed: 375 average time/residue: 0.4801 time to fit residues: 273.5148 Evaluate side-chains 387 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 315 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 4.9990 chunk 354 optimal weight: 30.0000 chunk 216 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 371 optimal weight: 5.9990 chunk 342 optimal weight: 9.9990 chunk 295 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 228 optimal weight: 0.1980 chunk 181 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30114 Z= 0.197 Angle : 0.528 14.059 40813 Z= 0.270 Chirality : 0.043 0.169 4572 Planarity : 0.005 0.051 5333 Dihedral : 6.048 83.776 4259 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.11 % Allowed : 12.97 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3764 helix: 1.08 (0.14), residues: 1557 sheet: 0.23 (0.22), residues: 557 loop : -0.35 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 119 HIS 0.005 0.001 HIS B 283 PHE 0.014 0.001 PHE A 230 TYR 0.020 0.001 TYR E 13 ARG 0.009 0.000 ARG A 130 ********************** 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 386 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 321 time to evaluate : 3.339 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6189 (mmt) cc_final: 0.5602 (mmm) REVERT: A 55 THR cc_start: 0.8852 (p) cc_final: 0.8649 (p) REVERT: A 114 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6971 (mm-30) REVERT: A 124 LYS cc_start: 0.7222 (mtmm) cc_final: 0.6701 (mmtp) REVERT: A 183 MET cc_start: 0.8867 (mtt) cc_final: 0.8281 (mtt) REVERT: A 209 MET cc_start: 0.7425 (mtp) cc_final: 0.7118 (mtp) REVERT: A 276 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6580 (ptpt) REVERT: A 393 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6699 (pp20) REVERT: A 456 GLU cc_start: 0.6461 (mt-10) cc_final: 0.6074 (mt-10) REVERT: A 491 ARG cc_start: 0.6520 (mmt180) cc_final: 0.5694 (ttp-110) REVERT: A 537 ASP cc_start: 0.6551 (t0) cc_final: 0.5944 (m-30) REVERT: A 542 LEU cc_start: 0.5946 (mt) cc_final: 0.5690 (mt) REVERT: A 546 GLU cc_start: 0.5853 (pp20) cc_final: 0.5511 (tm-30) REVERT: B 130 ARG cc_start: 0.6707 (mtm110) cc_final: 0.6219 (mtp85) REVERT: B 154 ARG cc_start: 0.7360 (mtm110) cc_final: 0.6462 (mtt90) REVERT: B 248 ASP cc_start: 0.7118 (m-30) cc_final: 0.6779 (m-30) REVERT: B 329 ARG cc_start: 0.6491 (mmt-90) cc_final: 0.6190 (mmp80) REVERT: B 342 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7013 (mt-10) REVERT: B 409 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6449 (tp) REVERT: B 465 GLN cc_start: 0.5153 (mm-40) cc_final: 0.4726 (mm-40) REVERT: B 477 GLN cc_start: 0.4536 (pp30) cc_final: 0.3253 (mm-40) REVERT: B 485 GLU cc_start: 0.6066 (mm-30) cc_final: 0.4823 (tp30) REVERT: B 558 GLU cc_start: 0.6427 (tt0) cc_final: 0.5995 (mt-10) REVERT: C 1 MET cc_start: 0.6079 (mpp) cc_final: 0.5605 (mmm) REVERT: C 130 ARG cc_start: 0.7049 (ttp-110) cc_final: 0.6727 (mtm-85) REVERT: C 180 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7286 (mm-30) REVERT: C 209 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7441 (mtm) REVERT: C 393 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7016 (tt0) REVERT: C 424 TRP cc_start: 0.7469 (p90) cc_final: 0.6630 (p-90) REVERT: C 459 GLN cc_start: 0.7259 (mt0) cc_final: 0.7054 (mt0) REVERT: C 541 GLN cc_start: 0.6744 (mp-120) cc_final: 0.6437 (mt0) REVERT: C 546 GLU cc_start: 0.6784 (tp30) cc_final: 0.6479 (tp30) REVERT: C 550 ARG cc_start: 0.7108 (mmt180) cc_final: 0.6474 (mtm110) REVERT: D 5 LYS cc_start: 0.5533 (mmtt) cc_final: 0.5003 (tptt) REVERT: D 34 ASP cc_start: 0.7254 (m-30) cc_final: 0.7053 (m-30) REVERT: D 206 GLN cc_start: 0.6874 (tp40) cc_final: 0.6285 (mm-40) REVERT: D 410 ARG cc_start: 0.6218 (mtp180) cc_final: 0.5948 (mtp180) REVERT: D 461 LYS cc_start: 0.6700 (tttm) cc_final: 0.6145 (ttpt) REVERT: E 185 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6005 (pt0) REVERT: E 290 ASP cc_start: 0.7076 (t70) cc_final: 0.6825 (t70) REVERT: E 334 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: E 380 ASP cc_start: 0.6880 (m-30) cc_final: 0.6275 (m-30) REVERT: E 409 ARG cc_start: 0.6275 (ttm-80) cc_final: 0.5876 (mtm110) REVERT: E 468 GLU cc_start: 0.3307 (OUTLIER) cc_final: 0.3053 (pm20) REVERT: F 7 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6264 (mm-30) REVERT: F 96 ILE cc_start: 0.7733 (pt) cc_final: 0.7411 (tp) REVERT: F 162 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: F 206 GLN cc_start: 0.6626 (mt0) cc_final: 0.6106 (mp10) REVERT: F 280 ARG cc_start: 0.7788 (mtt180) cc_final: 0.6382 (mtm110) REVERT: F 305 LYS cc_start: 0.6977 (mmtm) cc_final: 0.6721 (mttm) REVERT: F 455 SER cc_start: 0.7844 (t) cc_final: 0.7245 (p) REVERT: F 461 LYS cc_start: 0.7032 (tttp) cc_final: 0.6713 (ttmm) REVERT: G 148 LYS cc_start: 0.5573 (pttt) cc_final: 0.5066 (mttt) REVERT: G 160 ARG cc_start: 0.5625 (mmm-85) cc_final: 0.5322 (tpt-90) REVERT: G 177 ARG cc_start: 0.6357 (ttp80) cc_final: 0.5596 (mtm-85) REVERT: G 185 GLN cc_start: 0.6159 (tp40) cc_final: 0.5683 (tp40) REVERT: H 93 LEU cc_start: 0.4478 (mt) cc_final: 0.4228 (mp) REVERT: J 143 GLN cc_start: 0.3357 (OUTLIER) cc_final: 0.2269 (tt0) REVERT: L 74 GLN cc_start: 0.5711 (tt0) cc_final: 0.5321 (mt0) REVERT: L 94 LEU cc_start: 0.5355 (OUTLIER) cc_final: 0.5017 (mm) REVERT: L 121 LEU cc_start: 0.6021 (tt) cc_final: 0.5699 (mp) REVERT: L 142 LEU cc_start: 0.5033 (pt) cc_final: 0.4660 (mt) outliers start: 65 outliers final: 51 residues processed: 370 average time/residue: 0.4845 time to fit residues: 271.6196 Evaluate side-chains 380 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 319 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 1.9990 chunk 315 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 296 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 304 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.101210 restraints weight = 38317.517| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.41 r_work: 0.2851 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30114 Z= 0.236 Angle : 0.541 10.502 40813 Z= 0.277 Chirality : 0.044 0.175 4572 Planarity : 0.005 0.050 5333 Dihedral : 6.050 83.821 4259 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.30 % Allowed : 12.94 % Favored : 84.76 % 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: 0.43 (0.14), residues: 3764 helix: 1.07 (0.14), residues: 1562 sheet: 0.22 (0.23), residues: 548 loop : -0.36 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 119 HIS 0.006 0.001 HIS B 283 PHE 0.017 0.002 PHE C 230 TYR 0.020 0.001 TYR E 13 ARG 0.008 0.000 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6813.29 seconds wall clock time: 123 minutes 24.16 seconds (7404.16 seconds total)