Starting phenix.real_space_refine on Mon Mar 18 22:31:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxb_13696/03_2024/7pxb_13696_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxb_13696/03_2024/7pxb_13696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxb_13696/03_2024/7pxb_13696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxb_13696/03_2024/7pxb_13696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxb_13696/03_2024/7pxb_13696_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxb_13696/03_2024/7pxb_13696_neut_updated.pdb" } resolution = 4.0 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= 0.002 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 18 5.49 5 Mg 6 5.21 5 S 67 5.16 5 C 13992 2.51 5 N 3842 2.21 5 O 4361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "C ARG 378": "NH1" <-> "NH2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C ARG 494": "NH1" <-> "NH2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "E ARG 380": "NH1" <-> "NH2" Residue "E GLU 455": "OE1" <-> "OE2" Residue "E ARG 494": "NH1" <-> "NH2" Residue "E GLU 579": "OE1" <-> "OE2" Residue "E ARG 580": "NH1" <-> "NH2" Residue "G GLU 4": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22286 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3650 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain breaks: 3 Chain: "B" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3719 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 22, 'TRANS': 453} Chain breaks: 1 Chain: "C" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3629 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 22, 'TRANS': 441} Chain breaks: 2 Chain: "D" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3542 Classifications: {'peptide': 452} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Chain: "E" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3719 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 22, 'TRANS': 453} Chain breaks: 1 Chain: "F" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3723 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 22, 'TRANS': 454} Chain breaks: 1 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" 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} Chain: "B" 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} 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} Chain: "D" 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} Chain: "E" 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} Chain: "F" 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: 11.39, per 1000 atoms: 0.51 Number of scatterers: 22286 At special positions: 0 Unit cell: (139.308, 155.194, 129.532, 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 67 16.00 P 18 15.00 Mg 6 11.99 O 4361 8.00 N 3842 7.00 C 13992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.73 Conformation dependent library (CDL) restraints added in 3.9 seconds 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 25 sheets defined 35.1% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 259 through 273 removed outlier: 4.198A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 299 through 317 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 345 through 361 removed outlier: 3.948A pdb=" N ILE A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 402 removed outlier: 4.535A pdb=" N VAL A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 442 through 452 Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.811A pdb=" N GLU A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 486 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 510 through 513 Processing helix chain 'A' and resid 516 through 536 Processing helix chain 'A' and resid 544 through 557 removed outlier: 3.701A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 567 through 577 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 260 through 273 Proline residue: B 271 - end of helix Processing helix chain 'B' and resid 275 through 281 Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 334 through 337 removed outlier: 4.221A pdb=" N LEU B 337 " --> pdb=" O GLY B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 392 through 400 Processing helix chain 'B' and resid 442 through 452 Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 471 through 487 Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 516 through 536 Processing helix chain 'B' and resid 544 through 560 removed outlier: 5.082A pdb=" N ASP B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 577 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 258 through 273 removed outlier: 3.535A pdb=" N ASP C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Proline residue: C 271 - end of helix Processing helix chain 'C' and resid 275 through 281 Processing helix chain 'C' and resid 299 through 313 Processing helix chain 'C' and resid 344 through 360 Processing helix chain 'C' and resid 389 through 391 No H-bonds generated for 'chain 'C' and resid 389 through 391' Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 423 through 426 No H-bonds generated for 'chain 'C' and resid 423 through 426' Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 491 through 493 No H-bonds generated for 'chain 'C' and resid 491 through 493' Processing helix chain 'C' and resid 510 through 513 Processing helix chain 'C' and resid 516 through 537 Processing helix chain 'C' and resid 544 through 553 removed outlier: 3.780A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 577 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 258 through 267 Processing helix chain 'D' and resid 269 through 280 removed outlier: 6.096A pdb=" N GLU D 276 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 314 Processing helix chain 'D' and resid 334 through 337 No H-bonds generated for 'chain 'D' and resid 334 through 337' Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 442 through 452 Processing helix chain 'D' and resid 461 through 465 Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 491 through 493 No H-bonds generated for 'chain 'D' and resid 491 through 493' Processing helix chain 'D' and resid 516 through 536 Processing helix chain 'D' and resid 544 through 558 Processing helix chain 'D' and resid 570 through 577 Processing helix chain 'E' and resid 132 through 134 No H-bonds generated for 'chain 'E' and resid 132 through 134' Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 235 through 242 Processing helix chain 'E' and resid 251 through 253 No H-bonds generated for 'chain 'E' and resid 251 through 253' Processing helix chain 'E' and resid 259 through 273 removed outlier: 4.187A pdb=" N LEU E 270 " --> pdb=" O ASP E 266 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 275 through 280 Processing helix chain 'E' and resid 299 through 317 removed outlier: 3.695A pdb=" N ALA E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 removed outlier: 3.943A pdb=" N TYR E 328 " --> pdb=" O GLU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 337 No H-bonds generated for 'chain 'E' and resid 335 through 337' Processing helix chain 'E' and resid 344 through 359 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 388 through 400 Proline residue: E 394 - end of helix Processing helix chain 'E' and resid 442 through 452 Processing helix chain 'E' and resid 461 through 466 removed outlier: 4.082A pdb=" N GLU E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 486 Processing helix chain 'E' and resid 491 through 493 No H-bonds generated for 'chain 'E' and resid 491 through 493' Processing helix chain 'E' and resid 516 through 536 Processing helix chain 'E' and resid 544 through 557 Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'F' and resid 190 through 192 No H-bonds generated for 'chain 'F' and resid 190 through 192' Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 258 through 273 removed outlier: 4.183A pdb=" N LEU F 270 " --> pdb=" O ASP F 266 " (cutoff:3.500A) Proline residue: F 271 - end of helix Processing helix chain 'F' and resid 275 through 281 Processing helix chain 'F' and resid 300 through 315 Processing helix chain 'F' and resid 324 through 327 No H-bonds generated for 'chain 'F' and resid 324 through 327' Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 345 through 359 Processing helix chain 'F' and resid 388 through 399 removed outlier: 5.489A pdb=" N VAL F 393 " --> pdb=" O THR F 390 " (cutoff:3.500A) Proline residue: F 394 - end of helix Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 423 through 426 No H-bonds generated for 'chain 'F' and resid 423 through 426' Processing helix chain 'F' and resid 442 through 452 Processing helix chain 'F' and resid 461 through 467 removed outlier: 4.388A pdb=" N GLU F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE F 467 " --> pdb=" O ASP F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 486 Processing helix chain 'F' and resid 510 through 513 Processing helix chain 'F' and resid 516 through 536 Processing helix chain 'F' and resid 544 through 559 removed outlier: 3.949A pdb=" N GLU F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 577 removed outlier: 4.424A pdb=" N GLY F 575 " --> pdb=" O ALA F 571 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS F 576 " --> pdb=" O ARG F 572 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.594A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR A 107 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR A 112 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 219 through 222 removed outlier: 6.824A pdb=" N LEU A 175 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE A 167 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG A 173 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 433 through 437 removed outlier: 8.551A pdb=" N VAL A 289 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 411 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU A 291 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY A 413 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLY A 293 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER A 415 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL A 366 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE A 412 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 368 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA A 414 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE A 370 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 506 through 509 removed outlier: 3.740A pdb=" N LEU A 496 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 583 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.648A pdb=" N ASP B 114 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR B 107 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR B 112 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 183 through 187 removed outlier: 6.438A pdb=" N VAL B 177 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU B 164 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP B 223 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 433 through 437 removed outlier: 7.788A pdb=" N VAL B 289 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL B 411 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 291 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY B 413 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLY B 293 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER B 415 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL B 366 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE B 412 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 368 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ALA B 414 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE B 370 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 506 through 509 Processing sheet with id= I, first strand: chain 'C' and resid 140 through 142 removed outlier: 6.825A pdb=" N ASP C 114 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR C 107 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR C 112 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 183 through 187 removed outlier: 3.918A pdb=" N GLU C 166 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 177 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU C 164 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER C 219 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU C 231 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP C 223 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA C 229 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 433 through 437 removed outlier: 8.476A pdb=" N VAL C 289 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL C 411 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU C 291 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY C 413 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N GLY C 293 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER C 415 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 366 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE C 412 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL C 368 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA C 414 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE C 370 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE C 369 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 330 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 506 through 509 removed outlier: 4.029A pdb=" N TYR C 583 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 140 through 142 removed outlier: 6.598A pdb=" N ASP D 114 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 183 through 187 removed outlier: 5.972A pdb=" N VAL D 177 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU D 164 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER D 219 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU D 231 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASP D 223 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA D 229 " --> pdb=" O ASP D 223 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 433 through 437 removed outlier: 6.853A pdb=" N VAL D 411 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU D 291 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY D 413 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N GLY D 293 " --> pdb=" O GLY D 413 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER D 415 " --> pdb=" O GLY D 293 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE D 369 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU D 330 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASP D 371 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE D 332 " --> pdb=" O ASP D 371 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 505 through 508 removed outlier: 3.827A pdb=" N THR D 499 " --> pdb=" O TYR D 583 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR D 583 " --> pdb=" O THR D 499 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 151 through 153 removed outlier: 4.198A pdb=" N GLU E 151 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR E 140 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP E 114 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N THR E 107 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR E 112 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 183 through 187 removed outlier: 5.766A pdb=" N VAL E 177 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU E 164 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU E 231 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP E 223 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA E 229 " --> pdb=" O ASP E 223 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 433 through 437 removed outlier: 3.655A pdb=" N VAL E 433 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL E 289 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL E 411 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU E 291 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY E 413 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N GLY E 293 " --> pdb=" O GLY E 413 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER E 415 " --> pdb=" O GLY E 293 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL E 366 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE E 412 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL E 368 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA E 414 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE E 370 " --> pdb=" O ALA E 414 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 584 through 586 removed outlier: 3.852A pdb=" N ARG E 585 " --> pdb=" O GLU E 497 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET E 508 " --> pdb=" O PHE E 495 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU E 497 " --> pdb=" O GLU E 506 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU E 506 " --> pdb=" O GLU E 497 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.879A pdb=" N ASP F 114 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N THR F 107 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR F 112 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 160 through 163 removed outlier: 4.007A pdb=" N GLU F 231 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP F 223 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA F 229 " --> pdb=" O ASP F 223 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 184 through 187 removed outlier: 3.596A pdb=" N GLU F 166 " --> pdb=" O LEU F 175 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 433 through 437 removed outlier: 6.281A pdb=" N VAL F 366 " --> pdb=" O ILE F 410 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE F 412 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL F 368 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA F 414 " --> pdb=" O VAL F 368 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE F 370 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU F 330 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP F 371 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE F 332 " --> pdb=" O ASP F 371 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 505 through 509 786 hydrogen bonds defined for protein. 2250 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: 7.47 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5988 1.33 - 1.45: 3482 1.45 - 1.57: 13039 1.57 - 1.69: 30 1.69 - 1.81: 116 Bond restraints: 22655 Sorted by residual: bond pdb=" C4 ATP F 701 " pdb=" C5 ATP F 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.94e+01 bond pdb=" C4 ATP C 701 " pdb=" C5 ATP C 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C4 ATP D 701 " pdb=" C5 ATP D 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C4 ATP E 701 " pdb=" C5 ATP E 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.76e+01 ... (remaining 22650 not shown) Histogram of bond angle deviations from ideal: 96.80 - 104.65: 428 104.65 - 112.51: 11853 112.51 - 120.36: 9380 120.36 - 128.22: 8908 128.22 - 136.07: 112 Bond angle restraints: 30681 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 117.31 22.56 1.00e+00 1.00e+00 5.09e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 117.65 22.22 1.00e+00 1.00e+00 4.94e+02 angle pdb=" PB ATP F 701 " pdb=" O3B ATP F 701 " pdb=" PG ATP F 701 " ideal model delta sigma weight residual 139.87 117.85 22.02 1.00e+00 1.00e+00 4.85e+02 angle pdb=" PB ATP E 701 " pdb=" O3B ATP E 701 " pdb=" PG ATP E 701 " ideal model delta sigma weight residual 139.87 117.94 21.93 1.00e+00 1.00e+00 4.81e+02 angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 119.41 20.46 1.00e+00 1.00e+00 4.19e+02 ... (remaining 30676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13286 18.00 - 35.99: 523 35.99 - 53.99: 121 53.99 - 71.99: 29 71.99 - 89.99: 36 Dihedral angle restraints: 13995 sinusoidal: 5851 harmonic: 8144 Sorted by residual: dihedral pdb=" CA LEU B 561 " pdb=" C LEU B 561 " pdb=" N PRO B 562 " pdb=" CA PRO B 562 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB GLU D 557 " pdb=" CG GLU D 557 " pdb=" CD GLU D 557 " pdb=" OE1 GLU D 557 " ideal model delta sinusoidal sigma weight residual 0.00 88.63 -88.63 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 183 " pdb=" CG GLU B 183 " pdb=" CD GLU B 183 " pdb=" OE1 GLU B 183 " ideal model delta sinusoidal sigma weight residual 0.00 -86.76 86.76 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 13992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2641 0.043 - 0.086: 571 0.086 - 0.128: 268 0.128 - 0.171: 4 0.171 - 0.214: 5 Chirality restraints: 3489 Sorted by residual: chirality pdb=" CA ILE C 435 " pdb=" N ILE C 435 " pdb=" C ILE C 435 " pdb=" CB ILE C 435 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE C 437 " pdb=" N ILE C 437 " pdb=" C ILE C 437 " pdb=" CB ILE C 437 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA LEU E 221 " pdb=" N LEU E 221 " pdb=" C LEU E 221 " pdb=" CB LEU E 221 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 3486 not shown) Planarity restraints: 3988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 229 " 0.029 2.00e-02 2.50e+03 5.91e-02 3.49e+01 pdb=" C ALA E 229 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA E 229 " 0.040 2.00e-02 2.50e+03 pdb=" N PHE E 230 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 334 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO B 335 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 335 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 335 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 334 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO E 335 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 335 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 335 " 0.022 5.00e-02 4.00e+02 ... (remaining 3985 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 223 2.60 - 3.17: 19403 3.17 - 3.75: 34761 3.75 - 4.32: 46917 4.32 - 4.90: 77242 Nonbonded interactions: 178546 Sorted by model distance: nonbonded pdb=" O1G ATP E 701 " pdb="MG MG E 702 " model vdw 2.022 2.170 nonbonded pdb=" O1B ATP D 701 " pdb="MG MG D 702 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR A 300 " pdb="MG MG A 702 " model vdw 2.133 2.170 nonbonded pdb=" OG1 THR E 300 " pdb="MG MG E 702 " model vdw 2.144 2.170 nonbonded pdb=" O1B ATP A 701 " pdb="MG MG A 702 " model vdw 2.145 2.170 ... (remaining 178541 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 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 701 through 702)) selection = (chain 'B' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 701 through 702)) selection = (chain 'C' and (resid 97 through 377 or resid 390 through 587 or resid 701 throu \ gh 702)) selection = chain 'D' selection = (chain 'E' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 701 through 702)) selection = (chain 'F' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 701 through 702)) } 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 group one per residue 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.540 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 56.350 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 22655 Z= 0.259 Angle : 0.734 22.561 30681 Z= 0.563 Chirality : 0.042 0.214 3489 Planarity : 0.003 0.059 3988 Dihedral : 11.582 89.987 8739 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 2.05 % Allowed : 5.27 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 1.14 (0.17), residues: 2792 helix: 2.09 (0.18), residues: 945 sheet: 0.23 (0.22), residues: 502 loop : 0.08 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 187 HIS 0.002 0.000 HIS B 323 PHE 0.008 0.001 PHE F 341 TYR 0.008 0.001 TYR B 449 ARG 0.002 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 273 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7264 (m) cc_final: 0.6971 (t) REVERT: A 396 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7548 (tt) REVERT: A 408 ASN cc_start: 0.6529 (OUTLIER) cc_final: 0.5392 (m110) REVERT: B 137 LYS cc_start: 0.6457 (ttmt) cc_final: 0.5855 (tptp) REVERT: B 384 VAL cc_start: 0.8206 (m) cc_final: 0.7672 (t) REVERT: C 314 MET cc_start: 0.6615 (tpt) cc_final: 0.6356 (tpt) REVERT: C 373 MET cc_start: 0.8430 (mmt) cc_final: 0.8207 (mpp) REVERT: C 420 MET cc_start: 0.7588 (mmm) cc_final: 0.7051 (mtm) REVERT: C 495 PHE cc_start: 0.5343 (t80) cc_final: 0.4023 (t80) REVERT: D 420 MET cc_start: 0.6935 (mtt) cc_final: 0.6560 (tpt) REVERT: D 524 ASP cc_start: 0.7654 (m-30) cc_final: 0.7381 (m-30) REVERT: E 122 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7192 (tpp) REVERT: E 124 LEU cc_start: 0.7571 (mp) cc_final: 0.6990 (mp) REVERT: E 389 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8598 (pp20) REVERT: F 316 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6742 (pm20) REVERT: F 373 MET cc_start: 0.8463 (tpp) cc_final: 0.8093 (tpp) outliers start: 49 outliers final: 14 residues processed: 316 average time/residue: 0.3680 time to fit residues: 176.0452 Evaluate side-chains 158 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 234 PRO Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain F residue 316 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 1.9990 chunk 211 optimal weight: 0.0770 chunk 117 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 253 optimal weight: 0.5980 overall best weight: 2.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 529 ASN A 539 GLN B 263 GLN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS B 521 ASN B 539 GLN B 546 HIS C 172 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS D 348 HIS D 416 ASN D 446 GLN D 520 GLN E 108 HIS E 408 ASN F 274 HIS F 348 HIS F 354 GLN F 395 GLN F 520 GLN F 546 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22655 Z= 0.307 Angle : 0.597 8.571 30681 Z= 0.310 Chirality : 0.043 0.186 3489 Planarity : 0.005 0.056 3988 Dihedral : 8.986 85.939 3315 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.09 % Allowed : 9.90 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.81 (0.16), residues: 2792 helix: 1.71 (0.18), residues: 946 sheet: 0.01 (0.22), residues: 516 loop : -0.01 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 570 HIS 0.006 0.001 HIS C 274 PHE 0.019 0.002 PHE C 495 TYR 0.014 0.002 TYR C 328 ARG 0.005 0.001 ARG E 543 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 141 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7624 (tt) REVERT: A 408 ASN cc_start: 0.6618 (OUTLIER) cc_final: 0.5413 (m110) REVERT: B 109 ASP cc_start: 0.8556 (p0) cc_final: 0.8079 (p0) REVERT: B 137 LYS cc_start: 0.6620 (ttmt) cc_final: 0.6015 (tptp) REVERT: B 384 VAL cc_start: 0.8651 (m) cc_final: 0.8106 (t) REVERT: C 314 MET cc_start: 0.6872 (tpt) cc_final: 0.6649 (tpt) REVERT: C 420 MET cc_start: 0.7563 (mmm) cc_final: 0.6974 (mtm) REVERT: D 97 PRO cc_start: 0.5760 (Cg_exo) cc_final: 0.5444 (Cg_endo) REVERT: D 269 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6660 (mp0) REVERT: D 314 MET cc_start: 0.6220 (ptt) cc_final: 0.4463 (tpt) REVERT: D 420 MET cc_start: 0.6883 (mtt) cc_final: 0.6450 (tpt) REVERT: D 524 ASP cc_start: 0.7730 (m-30) cc_final: 0.7464 (m-30) REVERT: D 536 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7325 (mt-10) REVERT: E 122 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7231 (tpp) REVERT: E 124 LEU cc_start: 0.7508 (mp) cc_final: 0.6689 (mt) REVERT: E 273 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8613 (mm) REVERT: E 389 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8572 (pp20) REVERT: F 316 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6832 (pm20) REVERT: F 371 ASP cc_start: 0.7980 (t0) cc_final: 0.7734 (t0) REVERT: F 373 MET cc_start: 0.8703 (tpp) cc_final: 0.8348 (tpp) outliers start: 50 outliers final: 29 residues processed: 182 average time/residue: 0.2827 time to fit residues: 85.6223 Evaluate side-chains 162 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 570 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 140 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 253 optimal weight: 0.3980 chunk 274 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 86 optimal weight: 0.4980 chunk 203 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 ASN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS E 274 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22655 Z= 0.167 Angle : 0.520 11.829 30681 Z= 0.264 Chirality : 0.041 0.196 3489 Planarity : 0.004 0.054 3988 Dihedral : 8.626 88.298 3312 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.30 % Allowed : 11.45 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.88 (0.17), residues: 2792 helix: 1.83 (0.18), residues: 943 sheet: -0.03 (0.22), residues: 519 loop : 0.02 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 570 HIS 0.003 0.000 HIS D 460 PHE 0.023 0.001 PHE B 155 TYR 0.009 0.001 TYR B 292 ARG 0.004 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 134 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.7106 (pp) cc_final: 0.6533 (pp) REVERT: A 396 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7548 (tt) REVERT: A 408 ASN cc_start: 0.6590 (OUTLIER) cc_final: 0.5418 (m110) REVERT: B 137 LYS cc_start: 0.6607 (ttmt) cc_final: 0.5920 (tptp) REVERT: B 384 VAL cc_start: 0.8566 (m) cc_final: 0.8037 (t) REVERT: C 314 MET cc_start: 0.7016 (tpt) cc_final: 0.6795 (tpt) REVERT: C 420 MET cc_start: 0.7609 (mmm) cc_final: 0.6988 (mtm) REVERT: D 97 PRO cc_start: 0.5747 (Cg_exo) cc_final: 0.5435 (Cg_endo) REVERT: D 314 MET cc_start: 0.6164 (ptt) cc_final: 0.4299 (tpt) REVERT: D 524 ASP cc_start: 0.7754 (m-30) cc_final: 0.7476 (m-30) REVERT: D 536 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7265 (mt-10) REVERT: E 122 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7318 (tpp) REVERT: E 124 LEU cc_start: 0.7550 (mp) cc_final: 0.6797 (mt) REVERT: E 233 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7692 (tp) REVERT: E 253 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7522 (t0) REVERT: E 273 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8364 (mm) REVERT: E 389 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8645 (pp20) REVERT: F 316 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6794 (pm20) REVERT: F 373 MET cc_start: 0.8728 (tpp) cc_final: 0.8359 (tpp) outliers start: 55 outliers final: 29 residues processed: 182 average time/residue: 0.2948 time to fit residues: 90.1445 Evaluate side-chains 157 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 570 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 250 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 254 optimal weight: 0.6980 chunk 269 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 241 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 521 ASN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 ASN D 546 HIS F 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 22655 Z= 0.437 Angle : 0.736 8.362 30681 Z= 0.382 Chirality : 0.046 0.187 3489 Planarity : 0.006 0.068 3988 Dihedral : 9.510 88.570 3312 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.18 % Allowed : 13.00 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.06 (0.16), residues: 2792 helix: 0.82 (0.17), residues: 962 sheet: -0.30 (0.22), residues: 519 loop : -0.48 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 570 HIS 0.010 0.002 HIS C 274 PHE 0.022 0.003 PHE B 272 TYR 0.028 0.003 TYR F 228 ARG 0.020 0.001 ARG D 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 115 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8457 (pp) REVERT: A 396 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7606 (tp) REVERT: A 408 ASN cc_start: 0.6912 (OUTLIER) cc_final: 0.5625 (m110) REVERT: B 384 VAL cc_start: 0.8924 (m) cc_final: 0.8528 (t) REVERT: C 420 MET cc_start: 0.7532 (mmm) cc_final: 0.6891 (mtm) REVERT: D 160 GLU cc_start: 0.7345 (tm-30) cc_final: 0.7070 (tm-30) REVERT: D 290 LEU cc_start: 0.8115 (tp) cc_final: 0.7886 (tt) REVERT: D 486 MET cc_start: 0.7458 (tpp) cc_final: 0.6857 (tpp) REVERT: D 555 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.5081 (m-80) REVERT: E 122 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7437 (tpp) REVERT: E 233 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8062 (tp) REVERT: E 253 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7666 (t0) REVERT: E 389 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8376 (pp20) REVERT: F 316 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: F 371 ASP cc_start: 0.8158 (t0) cc_final: 0.7821 (t0) REVERT: F 491 ASP cc_start: 0.6553 (OUTLIER) cc_final: 0.6192 (m-30) REVERT: G 1 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6234 (mtt) outliers start: 76 outliers final: 45 residues processed: 180 average time/residue: 0.2949 time to fit residues: 86.8781 Evaluate side-chains 161 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 105 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 491 ASP Chi-restraints excluded: chain F residue 570 TRP Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 224 optimal weight: 0.9980 chunk 153 optimal weight: 0.0980 chunk 3 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN B 274 HIS ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS F 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22655 Z= 0.204 Angle : 0.556 9.660 30681 Z= 0.285 Chirality : 0.042 0.166 3489 Planarity : 0.004 0.055 3988 Dihedral : 8.978 86.644 3311 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.67 % Allowed : 14.50 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.24 (0.16), residues: 2792 helix: 1.25 (0.17), residues: 959 sheet: -0.31 (0.22), residues: 500 loop : -0.37 (0.18), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 187 HIS 0.003 0.001 HIS D 460 PHE 0.030 0.002 PHE B 155 TYR 0.020 0.001 TYR F 228 ARG 0.005 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 121 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.6898 (pp) cc_final: 0.6558 (pp) REVERT: A 408 ASN cc_start: 0.6837 (OUTLIER) cc_final: 0.5657 (m110) REVERT: B 384 VAL cc_start: 0.8821 (m) cc_final: 0.8415 (t) REVERT: C 416 ASN cc_start: 0.8387 (p0) cc_final: 0.8033 (p0) REVERT: C 420 MET cc_start: 0.7514 (mmm) cc_final: 0.6855 (mtm) REVERT: D 290 LEU cc_start: 0.7975 (tp) cc_final: 0.7745 (tt) REVERT: D 524 ASP cc_start: 0.7681 (m-30) cc_final: 0.7457 (m-30) REVERT: E 122 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7397 (tpp) REVERT: E 182 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.6121 (pm20) REVERT: E 233 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7936 (tp) REVERT: E 389 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8420 (pp20) REVERT: E 580 ARG cc_start: 0.6781 (mmm-85) cc_final: 0.6336 (mmm-85) REVERT: F 371 ASP cc_start: 0.7999 (t0) cc_final: 0.7670 (t0) REVERT: G 1 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6314 (mtt) outliers start: 64 outliers final: 43 residues processed: 177 average time/residue: 0.2978 time to fit residues: 87.5672 Evaluate side-chains 154 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 105 time to evaluate : 4.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 570 TRP Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 90 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 269 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 22 optimal weight: 0.0050 chunk 89 optimal weight: 1.9990 chunk 141 optimal weight: 0.3980 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS F 521 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22655 Z= 0.208 Angle : 0.554 9.206 30681 Z= 0.283 Chirality : 0.042 0.146 3489 Planarity : 0.004 0.054 3988 Dihedral : 8.740 85.183 3306 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.01 % Allowed : 15.25 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2792 helix: 1.29 (0.17), residues: 968 sheet: -0.28 (0.22), residues: 496 loop : -0.41 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 187 HIS 0.003 0.001 HIS D 460 PHE 0.013 0.001 PHE E 353 TYR 0.016 0.001 TYR F 228 ARG 0.013 0.000 ARG F 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 108 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.6914 (pp) cc_final: 0.6634 (pp) REVERT: A 408 ASN cc_start: 0.6852 (OUTLIER) cc_final: 0.5710 (m110) REVERT: B 384 VAL cc_start: 0.8778 (m) cc_final: 0.8371 (t) REVERT: C 416 ASN cc_start: 0.8347 (p0) cc_final: 0.8054 (p0) REVERT: D 290 LEU cc_start: 0.7935 (tp) cc_final: 0.7720 (tt) REVERT: D 430 ARG cc_start: 0.3705 (OUTLIER) cc_final: 0.3388 (mpp-170) REVERT: D 524 ASP cc_start: 0.7659 (m-30) cc_final: 0.7438 (m-30) REVERT: E 122 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7400 (tpp) REVERT: E 182 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5986 (pm20) REVERT: E 233 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7957 (tp) REVERT: E 389 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8436 (pp20) REVERT: G 1 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6281 (mtt) outliers start: 72 outliers final: 52 residues processed: 172 average time/residue: 0.2925 time to fit residues: 84.1257 Evaluate side-chains 164 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 105 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 570 TRP Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 260 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 153 optimal weight: 0.0270 chunk 197 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 168 optimal weight: 0.1980 chunk 163 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS E 520 GLN ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22655 Z= 0.172 Angle : 0.532 9.234 30681 Z= 0.270 Chirality : 0.041 0.144 3489 Planarity : 0.004 0.052 3988 Dihedral : 8.618 85.469 3306 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.05 % Allowed : 15.50 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.36 (0.16), residues: 2792 helix: 1.45 (0.17), residues: 961 sheet: -0.34 (0.22), residues: 504 loop : -0.35 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 187 HIS 0.003 0.001 HIS D 460 PHE 0.011 0.001 PHE E 467 TYR 0.012 0.001 TYR F 228 ARG 0.011 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 116 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.6892 (pp) cc_final: 0.6676 (pp) REVERT: A 408 ASN cc_start: 0.6835 (OUTLIER) cc_final: 0.5703 (m110) REVERT: B 384 VAL cc_start: 0.8695 (m) cc_final: 0.8290 (t) REVERT: C 416 ASN cc_start: 0.8314 (p0) cc_final: 0.8038 (p0) REVERT: D 213 LYS cc_start: 0.5962 (tttt) cc_final: 0.5577 (mtmm) REVERT: D 290 LEU cc_start: 0.7895 (tp) cc_final: 0.7681 (tt) REVERT: D 524 ASP cc_start: 0.7629 (m-30) cc_final: 0.7402 (m-30) REVERT: D 555 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.5110 (m-80) REVERT: E 122 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7410 (tpp) REVERT: E 182 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.6018 (pm20) REVERT: E 233 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8208 (tp) REVERT: E 389 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8437 (pp20) REVERT: F 491 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6525 (m-30) REVERT: G 1 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6130 (mtt) outliers start: 73 outliers final: 56 residues processed: 181 average time/residue: 0.2750 time to fit residues: 83.7694 Evaluate side-chains 177 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 113 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 462 ASP Chi-restraints excluded: chain F residue 491 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 570 TRP Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 166 optimal weight: 0.9980 chunk 107 optimal weight: 0.0470 chunk 160 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22655 Z= 0.230 Angle : 0.552 9.293 30681 Z= 0.282 Chirality : 0.042 0.145 3489 Planarity : 0.004 0.052 3988 Dihedral : 8.689 89.182 3306 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.09 % Allowed : 15.59 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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 (0.16), residues: 2792 helix: 1.38 (0.17), residues: 964 sheet: -0.42 (0.22), residues: 509 loop : -0.37 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS C 274 PHE 0.027 0.001 PHE B 155 TYR 0.015 0.001 TYR F 228 ARG 0.013 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 112 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ASN cc_start: 0.6863 (OUTLIER) cc_final: 0.5749 (m110) REVERT: B 384 VAL cc_start: 0.8746 (m) cc_final: 0.8339 (t) REVERT: B 502 ASN cc_start: 0.6275 (t0) cc_final: 0.5668 (m-40) REVERT: C 416 ASN cc_start: 0.8339 (p0) cc_final: 0.8055 (p0) REVERT: D 182 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5607 (pm20) REVERT: D 213 LYS cc_start: 0.5943 (tttt) cc_final: 0.5578 (mtmm) REVERT: D 277 LEU cc_start: 0.8251 (mt) cc_final: 0.8033 (tt) REVERT: D 290 LEU cc_start: 0.7944 (tp) cc_final: 0.7706 (tt) REVERT: D 430 ARG cc_start: 0.3603 (OUTLIER) cc_final: 0.3180 (mpp-170) REVERT: D 524 ASP cc_start: 0.7647 (m-30) cc_final: 0.7443 (m-30) REVERT: D 555 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.5152 (m-80) REVERT: E 122 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7420 (tpp) REVERT: E 182 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.6164 (pm20) REVERT: E 233 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8163 (tp) REVERT: E 389 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8424 (pp20) REVERT: F 491 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6489 (m-30) REVERT: G 1 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6277 (mtt) outliers start: 74 outliers final: 57 residues processed: 179 average time/residue: 0.2881 time to fit residues: 85.7964 Evaluate side-chains 173 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 106 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 491 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 570 TRP Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 257 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 226 optimal weight: 0.0770 chunk 237 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22655 Z= 0.155 Angle : 0.526 9.451 30681 Z= 0.266 Chirality : 0.041 0.142 3489 Planarity : 0.004 0.060 3988 Dihedral : 8.526 89.784 3306 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.59 % Allowed : 16.01 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.44 (0.17), residues: 2792 helix: 1.60 (0.18), residues: 951 sheet: -0.36 (0.22), residues: 524 loop : -0.32 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 570 HIS 0.003 0.000 HIS D 460 PHE 0.033 0.001 PHE B 155 TYR 0.011 0.001 TYR F 228 ARG 0.013 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 118 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.8285 (pt) cc_final: 0.7099 (mt) REVERT: A 408 ASN cc_start: 0.6975 (OUTLIER) cc_final: 0.5915 (m110) REVERT: B 384 VAL cc_start: 0.8689 (m) cc_final: 0.8243 (t) REVERT: B 419 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7452 (t70) REVERT: B 502 ASN cc_start: 0.6130 (t0) cc_final: 0.5625 (m-40) REVERT: C 416 ASN cc_start: 0.8299 (p0) cc_final: 0.8034 (p0) REVERT: C 420 MET cc_start: 0.7802 (mmm) cc_final: 0.7348 (mmm) REVERT: D 182 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5750 (pm20) REVERT: D 213 LYS cc_start: 0.5909 (tttt) cc_final: 0.5628 (mtmm) REVERT: D 290 LEU cc_start: 0.7879 (tp) cc_final: 0.7671 (tt) REVERT: D 430 ARG cc_start: 0.3820 (OUTLIER) cc_final: 0.3107 (mpp-170) REVERT: D 555 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.5077 (m-80) REVERT: E 122 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7408 (tpp) REVERT: E 182 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.6047 (pm20) REVERT: E 389 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8443 (pp20) REVERT: G 1 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6123 (mtt) outliers start: 62 outliers final: 47 residues processed: 172 average time/residue: 0.2852 time to fit residues: 81.6471 Evaluate side-chains 165 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 109 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 570 TRP Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 264 optimal weight: 0.5980 chunk 161 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 277 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22655 Z= 0.250 Angle : 0.576 9.754 30681 Z= 0.296 Chirality : 0.042 0.283 3489 Planarity : 0.005 0.071 3988 Dihedral : 8.597 88.302 3304 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.80 % Allowed : 16.13 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2792 helix: 1.37 (0.17), residues: 964 sheet: -0.40 (0.22), residues: 515 loop : -0.39 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 570 HIS 0.004 0.001 HIS C 274 PHE 0.020 0.002 PHE E 353 TYR 0.014 0.001 TYR F 228 ARG 0.016 0.001 ARG A 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 108 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ASN cc_start: 0.6885 (OUTLIER) cc_final: 0.5774 (m110) REVERT: B 384 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8359 (t) REVERT: B 502 ASN cc_start: 0.6424 (t0) cc_final: 0.5817 (m-40) REVERT: C 416 ASN cc_start: 0.8316 (p0) cc_final: 0.8033 (p0) REVERT: C 420 MET cc_start: 0.7783 (mmm) cc_final: 0.7325 (mmm) REVERT: C 432 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.5371 (t70) REVERT: D 182 GLU cc_start: 0.6088 (OUTLIER) cc_final: 0.5622 (pm20) REVERT: D 213 LYS cc_start: 0.5992 (tttt) cc_final: 0.5694 (mtmm) REVERT: D 290 LEU cc_start: 0.7965 (tp) cc_final: 0.7734 (tt) REVERT: D 430 ARG cc_start: 0.3687 (OUTLIER) cc_final: 0.3063 (mpp-170) REVERT: D 555 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.5097 (m-80) REVERT: E 122 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7423 (tpp) REVERT: E 182 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6149 (pm20) REVERT: E 389 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8427 (pp20) REVERT: F 491 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6533 (m-30) REVERT: G 1 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6327 (mtt) outliers start: 67 outliers final: 52 residues processed: 165 average time/residue: 0.2773 time to fit residues: 77.0799 Evaluate side-chains 170 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 107 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain F residue 491 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 570 TRP Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 194 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.075516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.062458 restraints weight = 103892.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.062409 restraints weight = 61846.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.062539 restraints weight = 52539.909| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22655 Z= 0.287 Angle : 0.600 10.319 30681 Z= 0.308 Chirality : 0.043 0.197 3489 Planarity : 0.005 0.068 3988 Dihedral : 8.707 89.289 3304 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.97 % Allowed : 16.13 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2792 helix: 1.25 (0.17), residues: 962 sheet: -0.46 (0.23), residues: 470 loop : -0.54 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 570 HIS 0.004 0.001 HIS C 274 PHE 0.022 0.002 PHE E 353 TYR 0.016 0.002 TYR F 228 ARG 0.019 0.001 ARG A 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3435.87 seconds wall clock time: 63 minutes 48.73 seconds (3828.73 seconds total)