Starting phenix.real_space_refine on Sun Mar 17 21:28:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/03_2024/6b5v_7058_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/03_2024/6b5v_7058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/03_2024/6b5v_7058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/03_2024/6b5v_7058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/03_2024/6b5v_7058_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/03_2024/6b5v_7058_trim_updated.pdb" } resolution = 4.8 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.008 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 Ca 1 9.91 5 S 140 5.16 5 Cl 12 4.86 5 C 12276 2.51 5 N 3188 2.21 5 O 3316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" 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: 18933 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4709 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 23, 'TRANS': 565} Chain breaks: 1 Chain: "B" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4709 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 23, 'TRANS': 565} Chain breaks: 1 Chain: "D" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4709 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 23, 'TRANS': 565} Chain breaks: 1 Chain: "C" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4709 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 23, 'TRANS': 565} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' CA': 1, 'ECL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'ECL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'ECL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'ECL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.59, per 1000 atoms: 0.51 Number of scatterers: 18933 At special positions: 0 Unit cell: (128.7, 128.7, 118.8, 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) Ca 1 19.99 Cl 12 17.00 S 140 16.00 O 3316 8.00 N 3188 7.00 C 12276 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: 6.06 Conformation dependent library (CDL) restraints added in 3.3 seconds 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 4 sheets defined 48.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 38 through 46 removed outlier: 4.127A pdb=" N GLU A 42 " --> pdb=" O MET A 38 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.581A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 86' Processing helix chain 'A' and resid 94 through 97 No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 103 through 106 removed outlier: 4.337A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.917A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 133 through 138' Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.778A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.033A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 185' Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.710A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 253 through 261 removed outlier: 4.243A pdb=" N MET A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.930A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 326 through 329 No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 331 through 348 removed outlier: 3.547A pdb=" N TYR A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 396 removed outlier: 4.251A pdb=" N GLU A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 401 No H-bonds generated for 'chain 'A' and resid 398 through 401' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.587A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.648A pdb=" N VAL A 427 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A 430 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 432 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 433 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 434 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 435 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL A 436 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET A 442 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 444 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 445 " --> pdb=" O MET A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 470 removed outlier: 4.311A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 486 removed outlier: 4.351A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 494 removed outlier: 3.708A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 490 through 494' Processing helix chain 'A' and resid 498 through 514 removed outlier: 4.077A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 536 removed outlier: 3.713A pdb=" N LEU A 530 " --> pdb=" O TYR A 526 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 569 through 581 removed outlier: 3.979A pdb=" N PHE A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 605 removed outlier: 3.887A pdb=" N TRP A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 38 through 46 removed outlier: 4.127A pdb=" N GLU B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 64 through 67 No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.581A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 86' Processing helix chain 'B' and resid 94 through 97 No H-bonds generated for 'chain 'B' and resid 94 through 97' Processing helix chain 'B' and resid 103 through 106 removed outlier: 4.338A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 133 through 138 removed outlier: 3.917A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 133 through 138' Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.778A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.034A pdb=" N ILE B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 185' Processing helix chain 'B' and resid 212 through 220 removed outlier: 3.711A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 253 through 261 removed outlier: 4.243A pdb=" N MET B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.930A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 326 through 329 No H-bonds generated for 'chain 'B' and resid 326 through 329' Processing helix chain 'B' and resid 331 through 348 removed outlier: 3.547A pdb=" N TYR B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 347 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 348 " --> pdb=" O THR B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 396 removed outlier: 4.251A pdb=" N GLU B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 401 No H-bonds generated for 'chain 'B' and resid 398 through 401' Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.586A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.649A pdb=" N VAL B 427 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE B 430 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 432 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 433 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 434 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 435 " --> pdb=" O TYR B 432 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 436 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET B 442 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 444 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 445 " --> pdb=" O MET B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 470 removed outlier: 4.312A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG B 470 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 486 removed outlier: 4.351A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 removed outlier: 3.709A pdb=" N CYS B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 494' Processing helix chain 'B' and resid 498 through 514 removed outlier: 4.077A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR B 514 " --> pdb=" O ILE B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 536 removed outlier: 3.713A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 569 through 581 removed outlier: 3.979A pdb=" N PHE B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 605 removed outlier: 3.887A pdb=" N TRP B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'D' and resid 30 through 35 Processing helix chain 'D' and resid 38 through 46 removed outlier: 4.127A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 53 No H-bonds generated for 'chain 'D' and resid 51 through 53' Processing helix chain 'D' and resid 64 through 67 No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.581A pdb=" N ALA D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 82 through 86' Processing helix chain 'D' and resid 94 through 97 No H-bonds generated for 'chain 'D' and resid 94 through 97' Processing helix chain 'D' and resid 103 through 106 removed outlier: 4.337A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 133 through 138 removed outlier: 3.916A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 133 through 138' Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.778A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 4.033A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 179 through 185' Processing helix chain 'D' and resid 212 through 220 removed outlier: 3.709A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 253 through 261 removed outlier: 4.243A pdb=" N MET D 260 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.929A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 323 Processing helix chain 'D' and resid 326 through 329 No H-bonds generated for 'chain 'D' and resid 326 through 329' Processing helix chain 'D' and resid 331 through 348 removed outlier: 3.546A pdb=" N TYR D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS D 347 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 348 " --> pdb=" O THR D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 396 removed outlier: 4.252A pdb=" N GLU D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 401 No H-bonds generated for 'chain 'D' and resid 398 through 401' Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.586A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.649A pdb=" N VAL D 427 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE D 430 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D 432 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 433 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER D 434 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU D 435 " --> pdb=" O TYR D 432 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL D 436 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET D 442 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D 444 " --> pdb=" O VAL D 441 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 445 " --> pdb=" O MET D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 470 removed outlier: 4.312A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA D 469 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG D 470 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 486 removed outlier: 4.351A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 494 removed outlier: 3.709A pdb=" N CYS D 494 " --> pdb=" O LEU D 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 490 through 494' Processing helix chain 'D' and resid 498 through 514 removed outlier: 4.078A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE D 504 " --> pdb=" O VAL D 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 512 " --> pdb=" O PHE D 508 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR D 514 " --> pdb=" O ILE D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 536 removed outlier: 3.713A pdb=" N LEU D 530 " --> pdb=" O TYR D 526 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 566 Processing helix chain 'D' and resid 569 through 581 removed outlier: 3.980A pdb=" N PHE D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR D 581 " --> pdb=" O MET D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 605 removed outlier: 3.887A pdb=" N TRP D 593 " --> pdb=" O ARG D 589 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL D 597 " --> pdb=" O TRP D 593 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 38 through 46 removed outlier: 4.127A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 64 through 67 No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.581A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 86' Processing helix chain 'C' and resid 94 through 97 No H-bonds generated for 'chain 'C' and resid 94 through 97' Processing helix chain 'C' and resid 103 through 106 removed outlier: 4.338A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 121 through 123 No H-bonds generated for 'chain 'C' and resid 121 through 123' Processing helix chain 'C' and resid 133 through 138 removed outlier: 3.916A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 138' Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.777A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 removed outlier: 4.034A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 185' Processing helix chain 'C' and resid 212 through 220 removed outlier: 3.710A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 253 through 261 removed outlier: 4.243A pdb=" N MET C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.930A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 323 Processing helix chain 'C' and resid 326 through 329 No H-bonds generated for 'chain 'C' and resid 326 through 329' Processing helix chain 'C' and resid 331 through 348 removed outlier: 3.547A pdb=" N TYR C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS C 347 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 348 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 396 removed outlier: 4.252A pdb=" N GLU C 389 " --> pdb=" O ARG C 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 401 No H-bonds generated for 'chain 'C' and resid 398 through 401' Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.586A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.648A pdb=" N VAL C 427 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE C 430 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 432 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 433 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 434 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C 435 " --> pdb=" O TYR C 432 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL C 436 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET C 442 " --> pdb=" O THR C 439 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 444 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR C 445 " --> pdb=" O MET C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 470 removed outlier: 4.311A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU C 460 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG C 470 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 486 removed outlier: 4.351A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 494 removed outlier: 3.709A pdb=" N CYS C 494 " --> pdb=" O LEU C 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 490 through 494' Processing helix chain 'C' and resid 498 through 514 removed outlier: 4.077A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR C 514 " --> pdb=" O ILE C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 536 removed outlier: 3.712A pdb=" N LEU C 530 " --> pdb=" O TYR C 526 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 569 through 581 removed outlier: 3.979A pdb=" N PHE C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR C 581 " --> pdb=" O MET C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 605 removed outlier: 3.888A pdb=" N TRP C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL C 597 " --> pdb=" O TRP C 593 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing sheet with id= A, first strand: chain 'A' and resid 273 through 275 removed outlier: 3.782A pdb=" N THR A 274 " --> pdb=" O ASN A 635 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A 635 " --> pdb=" O THR A 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 273 through 275 removed outlier: 3.783A pdb=" N THR B 274 " --> pdb=" O ASN B 635 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN B 635 " --> pdb=" O THR B 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'D' and resid 273 through 275 removed outlier: 3.783A pdb=" N THR D 274 " --> pdb=" O ASN D 635 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN D 635 " --> pdb=" O THR D 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 273 through 275 removed outlier: 3.782A pdb=" N THR C 274 " --> pdb=" O ASN C 635 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN C 635 " --> pdb=" O THR C 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 384 hydrogen bonds defined for protein. 1032 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: 4.94 Time building geometry restraints manager: 6.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5999 1.34 - 1.46: 4556 1.46 - 1.58: 8589 1.58 - 1.70: 4 1.70 - 1.82: 240 Bond restraints: 19388 Sorted by residual: bond pdb=" C11 ECL B1001 " pdb=" C9 ECL B1001 " ideal model delta sigma weight residual 1.384 1.526 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C11 ECL C1001 " pdb=" C9 ECL C1001 " ideal model delta sigma weight residual 1.384 1.526 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C13 ECL D1001 " pdb=" C2 ECL D1001 " ideal model delta sigma weight residual 1.385 1.527 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C13 ECL A1001 " pdb=" C2 ECL A1001 " ideal model delta sigma weight residual 1.385 1.527 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C11 ECL A1001 " pdb=" C9 ECL A1001 " ideal model delta sigma weight residual 1.384 1.525 -0.141 2.00e-02 2.50e+03 5.00e+01 ... (remaining 19383 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.10: 477 106.10 - 113.26: 9864 113.26 - 120.42: 8716 120.42 - 127.58: 7055 127.58 - 134.74: 212 Bond angle restraints: 26324 Sorted by residual: angle pdb=" N ARG D 584 " pdb=" CA ARG D 584 " pdb=" C ARG D 584 " ideal model delta sigma weight residual 111.07 120.47 -9.40 1.07e+00 8.73e-01 7.71e+01 angle pdb=" N ARG B 584 " pdb=" CA ARG B 584 " pdb=" C ARG B 584 " ideal model delta sigma weight residual 111.07 120.45 -9.38 1.07e+00 8.73e-01 7.69e+01 angle pdb=" N ARG A 584 " pdb=" CA ARG A 584 " pdb=" C ARG A 584 " ideal model delta sigma weight residual 111.07 120.45 -9.38 1.07e+00 8.73e-01 7.69e+01 angle pdb=" N ARG C 584 " pdb=" CA ARG C 584 " pdb=" C ARG C 584 " ideal model delta sigma weight residual 111.07 120.44 -9.37 1.07e+00 8.73e-01 7.66e+01 angle pdb=" C MET A 608 " pdb=" N PRO A 609 " pdb=" CA PRO A 609 " ideal model delta sigma weight residual 119.78 126.56 -6.78 1.03e+00 9.43e-01 4.33e+01 ... (remaining 26319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 9965 14.38 - 28.76: 1035 28.76 - 43.15: 336 43.15 - 57.53: 96 57.53 - 71.91: 36 Dihedral angle restraints: 11468 sinusoidal: 4592 harmonic: 6876 Sorted by residual: dihedral pdb=" CA LEU B 88 " pdb=" C LEU B 88 " pdb=" N TYR B 89 " pdb=" CA TYR B 89 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LEU A 88 " pdb=" C LEU A 88 " pdb=" N TYR A 89 " pdb=" CA TYR A 89 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA LEU D 88 " pdb=" C LEU D 88 " pdb=" N TYR D 89 " pdb=" CA TYR D 89 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 11465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1894 0.048 - 0.095: 765 0.095 - 0.143: 241 0.143 - 0.191: 68 0.191 - 0.238: 16 Chirality restraints: 2984 Sorted by residual: chirality pdb=" CA ARG A 584 " pdb=" N ARG A 584 " pdb=" C ARG A 584 " pdb=" CB ARG A 584 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ARG B 584 " pdb=" N ARG B 584 " pdb=" C ARG B 584 " pdb=" CB ARG B 584 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG C 584 " pdb=" N ARG C 584 " pdb=" C ARG C 584 " pdb=" CB ARG C 584 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2981 not shown) Planarity restraints: 3316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 516 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO C 517 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 517 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 517 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 516 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO B 517 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 517 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 517 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 516 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO A 517 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " -0.035 5.00e-02 4.00e+02 ... (remaining 3313 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 6175 2.85 - 3.36: 17620 3.36 - 3.87: 29424 3.87 - 4.39: 32231 4.39 - 4.90: 51682 Nonbonded interactions: 137132 Sorted by model distance: nonbonded pdb=" O LYS C 54 " pdb=" OH TYR C 89 " model vdw 2.333 2.440 nonbonded pdb=" O LYS A 54 " pdb=" OH TYR A 89 " model vdw 2.333 2.440 nonbonded pdb=" O LYS B 54 " pdb=" OH TYR B 89 " model vdw 2.333 2.440 nonbonded pdb=" O LYS D 54 " pdb=" OH TYR D 89 " model vdw 2.334 2.440 nonbonded pdb=" O GLY B 422 " pdb=" OH TYR B 467 " model vdw 2.368 2.440 ... (remaining 137127 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 29 through 637 or resid 1001)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.480 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 46.410 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.110 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.008 0.142 19388 Z= 0.503 Angle : 1.235 10.471 26324 Z= 0.654 Chirality : 0.059 0.238 2984 Planarity : 0.008 0.064 3316 Dihedral : 14.290 71.912 7028 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.55 % Allowed : 14.35 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.14), residues: 2340 helix: -4.04 (0.10), residues: 936 sheet: -0.18 (0.67), residues: 56 loop : -2.72 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 629 HIS 0.005 0.001 HIS B 157 PHE 0.029 0.002 PHE C 574 TYR 0.025 0.002 TYR B 278 ARG 0.025 0.003 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 599 time to evaluate : 2.028 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: 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: 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 126 MET cc_start: 0.9034 (ttp) cc_final: 0.8753 (ppp) REVERT: A 252 ASN cc_start: 0.9223 (t0) cc_final: 0.9005 (t0) REVERT: A 302 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7368 (ttt180) REVERT: A 386 LEU cc_start: 0.8988 (tm) cc_final: 0.8626 (mt) REVERT: A 403 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7775 (tp30) REVERT: A 491 MET cc_start: 0.7159 (ttm) cc_final: 0.6956 (tmm) REVERT: A 509 HIS cc_start: 0.9078 (t70) cc_final: 0.8740 (t70) REVERT: A 603 MET cc_start: 0.8640 (tmt) cc_final: 0.8226 (tmm) REVERT: A 616 SER cc_start: 0.9293 (p) cc_final: 0.9021 (t) REVERT: B 326 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7711 (mmm-85) REVERT: B 386 LEU cc_start: 0.9132 (tm) cc_final: 0.8798 (mt) REVERT: B 403 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7923 (tp30) REVERT: B 509 HIS cc_start: 0.9060 (t70) cc_final: 0.8727 (t70) REVERT: B 535 GLU cc_start: 0.8201 (pp20) cc_final: 0.7917 (pp20) REVERT: B 578 MET cc_start: 0.9098 (tmt) cc_final: 0.8822 (tmm) REVERT: B 632 ARG cc_start: 0.8755 (ttp-170) cc_final: 0.8324 (tmm-80) REVERT: D 42 GLU cc_start: 0.8834 (pm20) cc_final: 0.8584 (pm20) REVERT: D 59 ARG cc_start: 0.8033 (tmm160) cc_final: 0.7576 (ttp80) REVERT: D 252 ASN cc_start: 0.9293 (t0) cc_final: 0.9083 (t0) REVERT: D 302 ARG cc_start: 0.8160 (mmt180) cc_final: 0.7313 (ttt180) REVERT: D 309 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8347 (tm-30) REVERT: D 326 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7772 (mmm-85) REVERT: D 386 LEU cc_start: 0.8813 (tm) cc_final: 0.8402 (mt) REVERT: D 403 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7772 (tp30) REVERT: D 442 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8081 (tmm) REVERT: D 497 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8429 (tpt) REVERT: D 509 HIS cc_start: 0.9108 (t70) cc_final: 0.8837 (t70) REVERT: D 520 LEU cc_start: 0.8202 (tp) cc_final: 0.7993 (tt) REVERT: D 535 GLU cc_start: 0.8237 (pp20) cc_final: 0.7946 (pp20) REVERT: D 562 PHE cc_start: 0.9263 (t80) cc_final: 0.9036 (t80) REVERT: D 603 MET cc_start: 0.8629 (tmt) cc_final: 0.8235 (tmm) REVERT: D 616 SER cc_start: 0.9232 (p) cc_final: 0.8788 (t) REVERT: C 42 GLU cc_start: 0.8833 (pm20) cc_final: 0.8573 (pm20) REVERT: C 59 ARG cc_start: 0.8060 (tmm160) cc_final: 0.7679 (ttp80) REVERT: C 260 MET cc_start: 0.8662 (mmp) cc_final: 0.8451 (mmp) REVERT: C 302 ARG cc_start: 0.8159 (mmt180) cc_final: 0.7308 (ttt180) REVERT: C 386 LEU cc_start: 0.9108 (tm) cc_final: 0.8774 (mt) REVERT: C 403 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7814 (tp30) REVERT: C 497 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8379 (ttm) REVERT: C 509 HIS cc_start: 0.9066 (t70) cc_final: 0.8744 (t70) REVERT: C 535 GLU cc_start: 0.8262 (pp20) cc_final: 0.8014 (pp20) REVERT: C 603 MET cc_start: 0.8637 (tmt) cc_final: 0.8235 (tmm) outliers start: 72 outliers final: 17 residues processed: 634 average time/residue: 0.3316 time to fit residues: 306.4780 Evaluate side-chains 453 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 433 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 HIS ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS A 513 GLN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 426 HIS B 513 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS D 513 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN C 426 HIS C 513 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19388 Z= 0.263 Angle : 0.764 7.603 26324 Z= 0.389 Chirality : 0.046 0.146 2984 Planarity : 0.005 0.045 3316 Dihedral : 7.960 59.608 2612 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.16), residues: 2340 helix: -2.82 (0.14), residues: 944 sheet: -0.08 (0.60), residues: 56 loop : -2.02 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 583 HIS 0.005 0.001 HIS A 636 PHE 0.032 0.002 PHE B 574 TYR 0.021 0.002 TYR D 547 ARG 0.007 0.001 ARG C 632 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 2.050 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.9366 (t0) cc_final: 0.9159 (t0) REVERT: A 340 MET cc_start: 0.8980 (ttm) cc_final: 0.8728 (ttm) REVERT: A 386 LEU cc_start: 0.9135 (tt) cc_final: 0.8674 (mt) REVERT: A 403 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7809 (tp30) REVERT: A 442 MET cc_start: 0.7808 (tmm) cc_final: 0.7550 (tmm) REVERT: A 491 MET cc_start: 0.7124 (ttm) cc_final: 0.6886 (ttm) REVERT: A 497 MET cc_start: 0.9079 (ttt) cc_final: 0.8016 (tmm) REVERT: A 501 ILE cc_start: 0.9583 (pt) cc_final: 0.9276 (pt) REVERT: A 509 HIS cc_start: 0.9121 (t70) cc_final: 0.8624 (t70) REVERT: A 578 MET cc_start: 0.9110 (ttt) cc_final: 0.8790 (tmm) REVERT: A 603 MET cc_start: 0.8842 (ttt) cc_final: 0.8487 (tmm) REVERT: B 99 MET cc_start: 0.8777 (mpp) cc_final: 0.8483 (mpp) REVERT: B 340 MET cc_start: 0.9000 (ttm) cc_final: 0.8748 (ttm) REVERT: B 386 LEU cc_start: 0.9225 (tt) cc_final: 0.8767 (mt) REVERT: B 403 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7671 (tp30) REVERT: B 421 LEU cc_start: 0.9124 (tt) cc_final: 0.8865 (tt) REVERT: B 442 MET cc_start: 0.7683 (tmm) cc_final: 0.7202 (tmm) REVERT: B 497 MET cc_start: 0.9076 (ttt) cc_final: 0.8007 (tmm) REVERT: B 501 ILE cc_start: 0.9564 (pt) cc_final: 0.9286 (pt) REVERT: B 509 HIS cc_start: 0.9121 (t70) cc_final: 0.8664 (t70) REVERT: B 578 MET cc_start: 0.9058 (ttt) cc_final: 0.8787 (tmm) REVERT: B 587 GLN cc_start: 0.9179 (tp40) cc_final: 0.8921 (tp40) REVERT: B 596 GLN cc_start: 0.9326 (mt0) cc_final: 0.8820 (mm-40) REVERT: B 603 MET cc_start: 0.8800 (ttt) cc_final: 0.8462 (tmm) REVERT: D 99 MET cc_start: 0.8681 (mpp) cc_final: 0.8231 (mpp) REVERT: D 126 MET cc_start: 0.8963 (ppp) cc_final: 0.8741 (ppp) REVERT: D 178 ILE cc_start: 0.9161 (pt) cc_final: 0.8948 (tp) REVERT: D 252 ASN cc_start: 0.9358 (t0) cc_final: 0.9155 (t0) REVERT: D 260 MET cc_start: 0.9092 (mmp) cc_final: 0.8804 (mmp) REVERT: D 386 LEU cc_start: 0.8955 (tt) cc_final: 0.8435 (mt) REVERT: D 403 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7702 (tp30) REVERT: D 442 MET cc_start: 0.7771 (tmm) cc_final: 0.7358 (tmm) REVERT: D 497 MET cc_start: 0.9034 (ttt) cc_final: 0.7906 (tmm) REVERT: D 501 ILE cc_start: 0.9581 (pt) cc_final: 0.9298 (pt) REVERT: D 509 HIS cc_start: 0.9168 (t70) cc_final: 0.8741 (t70) REVERT: D 603 MET cc_start: 0.8844 (ttt) cc_final: 0.8402 (tmm) REVERT: C 99 MET cc_start: 0.8688 (mpp) cc_final: 0.8234 (mpp) REVERT: C 126 MET cc_start: 0.8992 (ppp) cc_final: 0.8764 (ppp) REVERT: C 178 ILE cc_start: 0.9162 (pt) cc_final: 0.8951 (tp) REVERT: C 260 MET cc_start: 0.9061 (mmp) cc_final: 0.8820 (mmp) REVERT: C 340 MET cc_start: 0.9002 (ttm) cc_final: 0.8745 (ttm) REVERT: C 386 LEU cc_start: 0.9253 (tt) cc_final: 0.8826 (mt) REVERT: C 403 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7808 (tp30) REVERT: C 442 MET cc_start: 0.7723 (tmm) cc_final: 0.7247 (tmm) REVERT: C 475 LEU cc_start: 0.8616 (tt) cc_final: 0.8400 (tt) REVERT: C 497 MET cc_start: 0.9071 (ttt) cc_final: 0.7942 (tmm) REVERT: C 501 ILE cc_start: 0.9572 (pt) cc_final: 0.9288 (pt) REVERT: C 509 HIS cc_start: 0.9128 (t70) cc_final: 0.8695 (t70) REVERT: C 577 MET cc_start: 0.8307 (tpt) cc_final: 0.8080 (tpt) REVERT: C 587 GLN cc_start: 0.9149 (tp40) cc_final: 0.8919 (tp40) REVERT: C 603 MET cc_start: 0.8747 (ttt) cc_final: 0.8436 (tmm) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.2691 time to fit residues: 202.8746 Evaluate side-chains 347 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 175 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 187 optimal weight: 40.0000 chunk 209 optimal weight: 4.9990 chunk 71 optimal weight: 0.0770 chunk 169 optimal weight: 0.6980 overall best weight: 2.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN B 73 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 513 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 GLN C 73 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19388 Z= 0.166 Angle : 0.663 7.305 26324 Z= 0.328 Chirality : 0.043 0.147 2984 Planarity : 0.004 0.055 3316 Dihedral : 7.044 56.700 2612 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.16), residues: 2340 helix: -2.06 (0.15), residues: 956 sheet: 0.29 (0.60), residues: 56 loop : -1.79 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 286 HIS 0.005 0.001 HIS C 84 PHE 0.024 0.001 PHE B 574 TYR 0.012 0.001 TYR A 89 ARG 0.005 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 2.122 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8544 (mpp) cc_final: 0.8113 (mpp) REVERT: A 126 MET cc_start: 0.8955 (ttm) cc_final: 0.8712 (ttm) REVERT: A 159 LEU cc_start: 0.7204 (tp) cc_final: 0.6951 (tt) REVERT: A 252 ASN cc_start: 0.9276 (t0) cc_final: 0.8761 (t0) REVERT: A 310 GLN cc_start: 0.8540 (tp40) cc_final: 0.8074 (tp40) REVERT: A 386 LEU cc_start: 0.9062 (tt) cc_final: 0.8841 (mt) REVERT: A 403 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7586 (tp30) REVERT: A 442 MET cc_start: 0.7929 (tmm) cc_final: 0.7666 (tmm) REVERT: A 466 MET cc_start: 0.8978 (ptm) cc_final: 0.8579 (ttp) REVERT: A 485 MET cc_start: 0.8638 (ppp) cc_final: 0.8164 (ttp) REVERT: A 497 MET cc_start: 0.9122 (ttt) cc_final: 0.8160 (tmm) REVERT: A 501 ILE cc_start: 0.9531 (pt) cc_final: 0.9222 (pt) REVERT: A 509 HIS cc_start: 0.9136 (t70) cc_final: 0.8661 (t-170) REVERT: A 572 ASN cc_start: 0.8032 (m110) cc_final: 0.7740 (m110) REVERT: A 578 MET cc_start: 0.8990 (ttt) cc_final: 0.8697 (tmm) REVERT: A 587 GLN cc_start: 0.9167 (tp40) cc_final: 0.8902 (tp40) REVERT: A 596 GLN cc_start: 0.9344 (mm110) cc_final: 0.9091 (mm110) REVERT: A 603 MET cc_start: 0.8672 (ttt) cc_final: 0.8340 (tmm) REVERT: B 386 LEU cc_start: 0.9210 (tt) cc_final: 0.8799 (mt) REVERT: B 403 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7551 (tp30) REVERT: B 442 MET cc_start: 0.7742 (tmm) cc_final: 0.7305 (tmm) REVERT: B 466 MET cc_start: 0.8993 (ptm) cc_final: 0.8629 (ttp) REVERT: B 497 MET cc_start: 0.9087 (ttt) cc_final: 0.8064 (tmm) REVERT: B 501 ILE cc_start: 0.9534 (pt) cc_final: 0.9218 (pt) REVERT: B 509 HIS cc_start: 0.9115 (t70) cc_final: 0.8666 (t-170) REVERT: B 587 GLN cc_start: 0.9114 (tp40) cc_final: 0.8895 (tp40) REVERT: B 603 MET cc_start: 0.8729 (ttt) cc_final: 0.8395 (tmm) REVERT: B 632 ARG cc_start: 0.8729 (ttp-170) cc_final: 0.8318 (tmm-80) REVERT: D 99 MET cc_start: 0.8665 (mpp) cc_final: 0.8182 (mpp) REVERT: D 252 ASN cc_start: 0.9274 (t0) cc_final: 0.8748 (t0) REVERT: D 310 GLN cc_start: 0.8586 (tp40) cc_final: 0.8158 (tp40) REVERT: D 403 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7428 (tp30) REVERT: D 442 MET cc_start: 0.7892 (tmm) cc_final: 0.7527 (tmm) REVERT: D 485 MET cc_start: 0.8747 (ppp) cc_final: 0.8076 (ttp) REVERT: D 497 MET cc_start: 0.9210 (ttt) cc_final: 0.8212 (tmm) REVERT: D 501 ILE cc_start: 0.9544 (pt) cc_final: 0.9218 (pt) REVERT: D 509 HIS cc_start: 0.9166 (t70) cc_final: 0.8745 (t-170) REVERT: D 578 MET cc_start: 0.9071 (tmm) cc_final: 0.8804 (tmm) REVERT: D 587 GLN cc_start: 0.9152 (tp40) cc_final: 0.8914 (tp40) REVERT: D 603 MET cc_start: 0.8767 (ttt) cc_final: 0.8332 (tmm) REVERT: C 41 GLN cc_start: 0.9304 (mp-120) cc_final: 0.9068 (mp10) REVERT: C 99 MET cc_start: 0.8628 (mpp) cc_final: 0.8135 (mpp) REVERT: C 403 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7549 (tp30) REVERT: C 442 MET cc_start: 0.7830 (tmm) cc_final: 0.7408 (tmm) REVERT: C 466 MET cc_start: 0.8997 (ptm) cc_final: 0.8600 (ttp) REVERT: C 485 MET cc_start: 0.8686 (ppp) cc_final: 0.8414 (ptm) REVERT: C 497 MET cc_start: 0.9113 (ttt) cc_final: 0.8101 (tmm) REVERT: C 501 ILE cc_start: 0.9535 (pt) cc_final: 0.9218 (pt) REVERT: C 509 HIS cc_start: 0.9131 (t70) cc_final: 0.8701 (t-170) REVERT: C 587 GLN cc_start: 0.9146 (tp40) cc_final: 0.8889 (tp40) REVERT: C 596 GLN cc_start: 0.9412 (mt0) cc_final: 0.8818 (mm-40) REVERT: C 603 MET cc_start: 0.8716 (ttt) cc_final: 0.8360 (tmm) outliers start: 0 outliers final: 0 residues processed: 495 average time/residue: 0.2738 time to fit residues: 209.4970 Evaluate side-chains 362 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 100 optimal weight: 0.3980 chunk 141 optimal weight: 2.9990 chunk 211 optimal weight: 0.0980 chunk 224 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 84 HIS ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN B 41 GLN B 84 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN D 84 HIS ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19388 Z= 0.143 Angle : 0.650 8.247 26324 Z= 0.311 Chirality : 0.042 0.147 2984 Planarity : 0.003 0.048 3316 Dihedral : 6.540 54.988 2612 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.17), residues: 2340 helix: -1.78 (0.15), residues: 984 sheet: 0.62 (0.62), residues: 56 loop : -1.77 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 286 HIS 0.004 0.001 HIS A 84 PHE 0.022 0.001 PHE D 574 TYR 0.010 0.001 TYR B 89 ARG 0.006 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 2.103 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: 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: symmetry clash REVERT: A 80 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8951 (mp0) REVERT: A 126 MET cc_start: 0.9002 (ttm) cc_final: 0.8704 (ttm) REVERT: A 132 LEU cc_start: 0.9298 (tp) cc_final: 0.8999 (pp) REVERT: A 159 LEU cc_start: 0.7164 (tp) cc_final: 0.6868 (tt) REVERT: A 252 ASN cc_start: 0.9177 (t0) cc_final: 0.8717 (t0) REVERT: A 310 GLN cc_start: 0.8548 (tp40) cc_final: 0.8122 (tp40) REVERT: A 403 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7406 (tp30) REVERT: A 442 MET cc_start: 0.7999 (tmm) cc_final: 0.7748 (tmm) REVERT: A 466 MET cc_start: 0.9000 (ptm) cc_final: 0.8649 (ttp) REVERT: A 497 MET cc_start: 0.9152 (ttt) cc_final: 0.8211 (tmm) REVERT: A 501 ILE cc_start: 0.9494 (pt) cc_final: 0.9166 (pt) REVERT: A 509 HIS cc_start: 0.9128 (t70) cc_final: 0.8879 (t70) REVERT: A 535 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 572 ASN cc_start: 0.7943 (m110) cc_final: 0.7510 (m110) REVERT: A 578 MET cc_start: 0.8886 (ttt) cc_final: 0.8629 (tmm) REVERT: A 587 GLN cc_start: 0.9155 (tp40) cc_final: 0.8931 (tp40) REVERT: A 603 MET cc_start: 0.8600 (ttt) cc_final: 0.8306 (tmm) REVERT: A 632 ARG cc_start: 0.8650 (ttp-170) cc_final: 0.8374 (tmm-80) REVERT: B 126 MET cc_start: 0.8997 (ppp) cc_final: 0.8761 (ppp) REVERT: B 386 LEU cc_start: 0.9194 (tt) cc_final: 0.8804 (mt) REVERT: B 403 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7407 (tp30) REVERT: B 442 MET cc_start: 0.7800 (tmm) cc_final: 0.7390 (tmm) REVERT: B 466 MET cc_start: 0.9011 (ptm) cc_final: 0.8700 (ttp) REVERT: B 497 MET cc_start: 0.9106 (ttt) cc_final: 0.8140 (tmm) REVERT: B 501 ILE cc_start: 0.9485 (pt) cc_final: 0.9078 (pt) REVERT: B 509 HIS cc_start: 0.9123 (t70) cc_final: 0.8610 (t-170) REVERT: B 535 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8057 (tm-30) REVERT: B 577 MET cc_start: 0.8047 (tpt) cc_final: 0.7796 (tpt) REVERT: B 587 GLN cc_start: 0.9097 (tp40) cc_final: 0.8746 (tp40) REVERT: B 603 MET cc_start: 0.8655 (ttt) cc_final: 0.8365 (tmm) REVERT: D 59 ARG cc_start: 0.7541 (ttp80) cc_final: 0.7125 (ttp80) REVERT: D 252 ASN cc_start: 0.9186 (t0) cc_final: 0.8709 (t0) REVERT: D 310 GLN cc_start: 0.8595 (tp40) cc_final: 0.8206 (tp40) REVERT: D 340 MET cc_start: 0.8742 (ttm) cc_final: 0.8499 (ttm) REVERT: D 403 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7313 (tp30) REVERT: D 442 MET cc_start: 0.7916 (tmm) cc_final: 0.7578 (tmm) REVERT: D 485 MET cc_start: 0.8692 (ppp) cc_final: 0.8402 (ttp) REVERT: D 497 MET cc_start: 0.9222 (ttt) cc_final: 0.8412 (tmm) REVERT: D 501 ILE cc_start: 0.9498 (pt) cc_final: 0.9088 (pt) REVERT: D 509 HIS cc_start: 0.9152 (t70) cc_final: 0.8710 (t-170) REVERT: D 535 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8044 (tm-30) REVERT: D 578 MET cc_start: 0.9049 (tmm) cc_final: 0.8784 (tmm) REVERT: D 587 GLN cc_start: 0.9008 (tp40) cc_final: 0.8718 (tp40) REVERT: D 603 MET cc_start: 0.8648 (ttt) cc_final: 0.8273 (tmm) REVERT: C 99 MET cc_start: 0.8616 (mpp) cc_final: 0.8079 (mpp) REVERT: C 350 ARG cc_start: 0.8298 (tpt170) cc_final: 0.7673 (tpt-90) REVERT: C 403 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7611 (tp30) REVERT: C 466 MET cc_start: 0.8975 (ptm) cc_final: 0.8646 (ttp) REVERT: C 485 MET cc_start: 0.8761 (ppp) cc_final: 0.8222 (ttp) REVERT: C 491 MET cc_start: 0.8132 (ttm) cc_final: 0.7780 (tmm) REVERT: C 497 MET cc_start: 0.9164 (ttt) cc_final: 0.8304 (tmm) REVERT: C 501 ILE cc_start: 0.9491 (pt) cc_final: 0.9124 (pt) REVERT: C 509 HIS cc_start: 0.9121 (t70) cc_final: 0.8862 (t70) REVERT: C 578 MET cc_start: 0.9130 (tmm) cc_final: 0.8907 (tmm) REVERT: C 587 GLN cc_start: 0.9094 (tp40) cc_final: 0.8701 (tp40) REVERT: C 596 GLN cc_start: 0.9445 (mt0) cc_final: 0.8791 (mm-40) REVERT: C 603 MET cc_start: 0.8589 (ttt) cc_final: 0.8319 (tmm) REVERT: C 635 ASN cc_start: 0.9155 (t0) cc_final: 0.8950 (t0) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.2760 time to fit residues: 214.1700 Evaluate side-chains 371 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.9980 chunk 127 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 166 optimal weight: 0.3980 chunk 92 optimal weight: 6.9990 chunk 191 optimal weight: 0.0050 chunk 155 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 201 optimal weight: 0.0270 chunk 56 optimal weight: 4.9990 overall best weight: 0.4852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 118 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19388 Z= 0.124 Angle : 0.651 9.435 26324 Z= 0.300 Chirality : 0.041 0.150 2984 Planarity : 0.003 0.046 3316 Dihedral : 5.966 52.563 2612 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.16), residues: 2340 helix: -1.55 (0.15), residues: 1000 sheet: 0.93 (0.64), residues: 56 loop : -1.90 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 286 HIS 0.003 0.000 HIS C 157 PHE 0.014 0.001 PHE C 574 TYR 0.006 0.001 TYR D 328 ARG 0.004 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 517 time to evaluate : 2.228 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: 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: symmetry clash REVERT: A 99 MET cc_start: 0.8611 (mpp) cc_final: 0.8291 (mpp) REVERT: A 126 MET cc_start: 0.9037 (ttm) cc_final: 0.8761 (ttm) REVERT: A 132 LEU cc_start: 0.9283 (tp) cc_final: 0.8994 (pp) REVERT: A 252 ASN cc_start: 0.9035 (t0) cc_final: 0.8534 (t0) REVERT: A 260 MET cc_start: 0.9227 (mmp) cc_final: 0.8847 (mmm) REVERT: A 403 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7296 (tp30) REVERT: A 442 MET cc_start: 0.7916 (tmm) cc_final: 0.7709 (tmm) REVERT: A 466 MET cc_start: 0.8892 (ptm) cc_final: 0.8686 (ttp) REVERT: A 497 MET cc_start: 0.9176 (ttt) cc_final: 0.8210 (tmm) REVERT: A 501 ILE cc_start: 0.9440 (pt) cc_final: 0.9073 (pt) REVERT: A 509 HIS cc_start: 0.9095 (t70) cc_final: 0.8887 (t-90) REVERT: A 535 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A 587 GLN cc_start: 0.9127 (tp40) cc_final: 0.8885 (tp40) REVERT: A 596 GLN cc_start: 0.9324 (mm110) cc_final: 0.9102 (mm110) REVERT: A 603 MET cc_start: 0.8530 (ttt) cc_final: 0.8269 (tmm) REVERT: B 126 MET cc_start: 0.8921 (ppp) cc_final: 0.8609 (ppp) REVERT: B 260 MET cc_start: 0.9181 (mmp) cc_final: 0.8902 (mmm) REVERT: B 386 LEU cc_start: 0.9186 (tt) cc_final: 0.8842 (mt) REVERT: B 403 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7404 (tp30) REVERT: B 421 LEU cc_start: 0.9249 (tt) cc_final: 0.9003 (tt) REVERT: B 442 MET cc_start: 0.8006 (tmm) cc_final: 0.7574 (tmm) REVERT: B 466 MET cc_start: 0.8909 (ptm) cc_final: 0.8702 (ttp) REVERT: B 485 MET cc_start: 0.8594 (ppp) cc_final: 0.8273 (ttp) REVERT: B 497 MET cc_start: 0.9204 (ttt) cc_final: 0.8198 (tmm) REVERT: B 501 ILE cc_start: 0.9433 (pt) cc_final: 0.9099 (pt) REVERT: B 509 HIS cc_start: 0.9084 (t70) cc_final: 0.8556 (t-170) REVERT: B 587 GLN cc_start: 0.9037 (tp40) cc_final: 0.8663 (tp40) REVERT: B 596 GLN cc_start: 0.9351 (mt0) cc_final: 0.8543 (mm-40) REVERT: B 603 MET cc_start: 0.8608 (ttt) cc_final: 0.8329 (tmm) REVERT: D 59 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7197 (ttp80) REVERT: D 99 MET cc_start: 0.8711 (mpp) cc_final: 0.8289 (mpp) REVERT: D 252 ASN cc_start: 0.9040 (t0) cc_final: 0.8537 (t0) REVERT: D 260 MET cc_start: 0.9235 (mmp) cc_final: 0.8866 (mmm) REVERT: D 403 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7225 (tp30) REVERT: D 442 MET cc_start: 0.8102 (tmm) cc_final: 0.7838 (tmm) REVERT: D 497 MET cc_start: 0.9227 (ttt) cc_final: 0.8370 (tmm) REVERT: D 501 ILE cc_start: 0.9455 (pt) cc_final: 0.9106 (pt) REVERT: D 509 HIS cc_start: 0.9147 (t70) cc_final: 0.8627 (t-170) REVERT: D 578 MET cc_start: 0.8973 (tmm) cc_final: 0.8510 (tmm) REVERT: D 587 GLN cc_start: 0.9043 (tp40) cc_final: 0.8632 (tp40) REVERT: D 603 MET cc_start: 0.8627 (ttt) cc_final: 0.8266 (tmm) REVERT: C 260 MET cc_start: 0.9235 (mmp) cc_final: 0.8905 (mmm) REVERT: C 403 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7397 (tp30) REVERT: C 421 LEU cc_start: 0.9201 (tt) cc_final: 0.8962 (tt) REVERT: C 442 MET cc_start: 0.7850 (tmm) cc_final: 0.7398 (tmm) REVERT: C 491 MET cc_start: 0.8034 (ttm) cc_final: 0.7627 (tmm) REVERT: C 497 MET cc_start: 0.9146 (ttt) cc_final: 0.8265 (tmm) REVERT: C 501 ILE cc_start: 0.9417 (pt) cc_final: 0.9078 (pt) REVERT: C 509 HIS cc_start: 0.9085 (t70) cc_final: 0.8837 (t70) REVERT: C 578 MET cc_start: 0.9168 (tmm) cc_final: 0.8762 (tmm) REVERT: C 587 GLN cc_start: 0.9083 (tp40) cc_final: 0.8641 (tp40) REVERT: C 596 GLN cc_start: 0.9492 (mt0) cc_final: 0.8826 (mm-40) REVERT: C 603 MET cc_start: 0.8598 (ttt) cc_final: 0.8305 (tmm) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.2715 time to fit residues: 218.7761 Evaluate side-chains 392 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19388 Z= 0.190 Angle : 0.687 9.484 26324 Z= 0.330 Chirality : 0.043 0.149 2984 Planarity : 0.004 0.049 3316 Dihedral : 6.261 52.035 2612 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.17), residues: 2340 helix: -1.38 (0.15), residues: 1040 sheet: 0.81 (0.64), residues: 56 loop : -1.83 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 593 HIS 0.005 0.001 HIS A 84 PHE 0.031 0.001 PHE C 574 TYR 0.016 0.001 TYR C 547 ARG 0.007 0.000 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 2.166 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8512 (mpp) cc_final: 0.8206 (mpp) REVERT: A 126 MET cc_start: 0.9007 (ttm) cc_final: 0.8585 (ttm) REVERT: A 159 LEU cc_start: 0.7506 (tp) cc_final: 0.7186 (tt) REVERT: A 252 ASN cc_start: 0.9081 (t0) cc_final: 0.8583 (t0) REVERT: A 260 MET cc_start: 0.9342 (mmp) cc_final: 0.8899 (mmm) REVERT: A 310 GLN cc_start: 0.8661 (tp40) cc_final: 0.8148 (tp40) REVERT: A 403 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7676 (tp30) REVERT: A 442 MET cc_start: 0.8137 (tmm) cc_final: 0.7891 (tmm) REVERT: A 466 MET cc_start: 0.9108 (ptm) cc_final: 0.8794 (ttp) REVERT: A 497 MET cc_start: 0.9261 (ttt) cc_final: 0.8356 (tmm) REVERT: A 501 ILE cc_start: 0.9534 (pt) cc_final: 0.9087 (pt) REVERT: A 509 HIS cc_start: 0.9085 (t70) cc_final: 0.8650 (t70) REVERT: A 535 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7983 (tm-30) REVERT: A 554 MET cc_start: 0.9286 (mmm) cc_final: 0.8992 (mmm) REVERT: A 572 ASN cc_start: 0.7899 (m110) cc_final: 0.7674 (m110) REVERT: A 587 GLN cc_start: 0.9127 (tp40) cc_final: 0.8866 (tp40) REVERT: A 596 GLN cc_start: 0.9375 (mm110) cc_final: 0.9149 (mm110) REVERT: A 603 MET cc_start: 0.8605 (ttt) cc_final: 0.8325 (tmm) REVERT: A 635 ASN cc_start: 0.9287 (t0) cc_final: 0.9075 (t0) REVERT: B 99 MET cc_start: 0.8646 (mpp) cc_final: 0.8236 (mpp) REVERT: B 126 MET cc_start: 0.8976 (ppp) cc_final: 0.8625 (ppp) REVERT: B 245 LYS cc_start: 0.9221 (mmmt) cc_final: 0.8995 (mmmm) REVERT: B 260 MET cc_start: 0.9227 (mmp) cc_final: 0.8794 (mmm) REVERT: B 403 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7710 (tp30) REVERT: B 442 MET cc_start: 0.7879 (tmm) cc_final: 0.7448 (tmm) REVERT: B 466 MET cc_start: 0.9116 (ptm) cc_final: 0.8754 (ttp) REVERT: B 485 MET cc_start: 0.8689 (ppp) cc_final: 0.8290 (ttp) REVERT: B 497 MET cc_start: 0.9212 (ttt) cc_final: 0.8265 (tmm) REVERT: B 501 ILE cc_start: 0.9515 (pt) cc_final: 0.9007 (pt) REVERT: B 509 HIS cc_start: 0.9107 (t70) cc_final: 0.8834 (t70) REVERT: B 535 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8103 (tm-30) REVERT: B 572 ASN cc_start: 0.8063 (m110) cc_final: 0.7775 (m110) REVERT: B 603 MET cc_start: 0.8637 (ttt) cc_final: 0.8336 (tmm) REVERT: B 635 ASN cc_start: 0.9264 (t0) cc_final: 0.9051 (t0) REVERT: D 59 ARG cc_start: 0.7635 (ttp80) cc_final: 0.7227 (ttp80) REVERT: D 99 MET cc_start: 0.8595 (mpp) cc_final: 0.8231 (mpp) REVERT: D 252 ASN cc_start: 0.9085 (t0) cc_final: 0.8578 (t0) REVERT: D 260 MET cc_start: 0.9359 (mmp) cc_final: 0.8937 (mmm) REVERT: D 403 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7650 (tp30) REVERT: D 442 MET cc_start: 0.8074 (tmm) cc_final: 0.7669 (tmm) REVERT: D 497 MET cc_start: 0.9305 (ttt) cc_final: 0.8408 (tmm) REVERT: D 501 ILE cc_start: 0.9508 (pt) cc_final: 0.9066 (pt) REVERT: D 509 HIS cc_start: 0.9112 (t70) cc_final: 0.8837 (t70) REVERT: D 535 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8106 (tm-30) REVERT: D 578 MET cc_start: 0.8946 (tmm) cc_final: 0.8667 (tmm) REVERT: D 587 GLN cc_start: 0.9022 (tp40) cc_final: 0.8598 (tp40) REVERT: D 596 GLN cc_start: 0.9382 (mm110) cc_final: 0.9144 (mm110) REVERT: D 603 MET cc_start: 0.8641 (ttt) cc_final: 0.8290 (tmm) REVERT: D 635 ASN cc_start: 0.9139 (t0) cc_final: 0.8938 (t0) REVERT: C 41 GLN cc_start: 0.9229 (mp10) cc_final: 0.9016 (mp10) REVERT: C 99 MET cc_start: 0.8592 (mpp) cc_final: 0.8225 (mpp) REVERT: C 260 MET cc_start: 0.9335 (mmp) cc_final: 0.8930 (mmm) REVERT: C 403 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7643 (tp30) REVERT: C 442 MET cc_start: 0.7975 (tmm) cc_final: 0.7605 (tmm) REVERT: C 491 MET cc_start: 0.8079 (ttm) cc_final: 0.7638 (tmm) REVERT: C 497 MET cc_start: 0.9243 (ttt) cc_final: 0.8391 (tmm) REVERT: C 501 ILE cc_start: 0.9515 (pt) cc_final: 0.9045 (pt) REVERT: C 509 HIS cc_start: 0.9086 (t70) cc_final: 0.8814 (t70) REVERT: C 572 ASN cc_start: 0.7936 (m110) cc_final: 0.7708 (m110) REVERT: C 603 MET cc_start: 0.8676 (ttt) cc_final: 0.8397 (tmm) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.2745 time to fit residues: 197.3649 Evaluate side-chains 375 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 10.0000 chunk 25 optimal weight: 0.0470 chunk 127 optimal weight: 20.0000 chunk 163 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 125 optimal weight: 0.0870 chunk 223 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 136 optimal weight: 0.0980 chunk 103 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19388 Z= 0.133 Angle : 0.670 9.160 26324 Z= 0.308 Chirality : 0.042 0.148 2984 Planarity : 0.003 0.048 3316 Dihedral : 5.802 50.214 2612 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.17), residues: 2340 helix: -1.36 (0.16), residues: 1032 sheet: 0.99 (0.65), residues: 56 loop : -1.65 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 583 HIS 0.003 0.000 HIS C 157 PHE 0.022 0.001 PHE C 574 TYR 0.008 0.001 TYR A 559 ARG 0.008 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 2.147 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: 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 99 MET cc_start: 0.8495 (mpp) cc_final: 0.8238 (mpp) REVERT: A 126 MET cc_start: 0.9075 (ttm) cc_final: 0.8699 (ttm) REVERT: A 252 ASN cc_start: 0.8952 (t0) cc_final: 0.8424 (t0) REVERT: A 260 MET cc_start: 0.9345 (mmp) cc_final: 0.8877 (mmm) REVERT: A 309 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8397 (tm-30) REVERT: A 403 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7357 (tp30) REVERT: A 442 MET cc_start: 0.8137 (tmm) cc_final: 0.7840 (tmm) REVERT: A 497 MET cc_start: 0.9262 (ttt) cc_final: 0.8362 (tmm) REVERT: A 501 ILE cc_start: 0.9451 (pt) cc_final: 0.9019 (pt) REVERT: A 509 HIS cc_start: 0.8992 (t70) cc_final: 0.8524 (t70) REVERT: A 535 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 587 GLN cc_start: 0.9132 (tp40) cc_final: 0.8899 (tp40) REVERT: A 596 GLN cc_start: 0.9326 (mm110) cc_final: 0.9087 (mm110) REVERT: A 603 MET cc_start: 0.8548 (ttt) cc_final: 0.8293 (tmm) REVERT: B 99 MET cc_start: 0.8628 (mpp) cc_final: 0.8212 (mpp) REVERT: B 132 LEU cc_start: 0.9334 (tp) cc_final: 0.8948 (pp) REVERT: B 245 LYS cc_start: 0.9223 (mmmt) cc_final: 0.9021 (mmmm) REVERT: B 260 MET cc_start: 0.9221 (mmp) cc_final: 0.8713 (mmm) REVERT: B 403 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7408 (tp30) REVERT: B 442 MET cc_start: 0.8027 (tmm) cc_final: 0.7592 (tmm) REVERT: B 497 MET cc_start: 0.9237 (ttt) cc_final: 0.8316 (tmm) REVERT: B 501 ILE cc_start: 0.9416 (pt) cc_final: 0.9016 (pt) REVERT: B 509 HIS cc_start: 0.9050 (t70) cc_final: 0.8637 (t70) REVERT: B 535 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 572 ASN cc_start: 0.7956 (m110) cc_final: 0.7616 (m110) REVERT: B 603 MET cc_start: 0.8597 (ttt) cc_final: 0.8327 (tmm) REVERT: D 34 ASP cc_start: 0.9025 (t0) cc_final: 0.8725 (t0) REVERT: D 59 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7322 (ttp80) REVERT: D 99 MET cc_start: 0.8566 (mpp) cc_final: 0.8250 (mpp) REVERT: D 132 LEU cc_start: 0.9354 (tp) cc_final: 0.9015 (pp) REVERT: D 252 ASN cc_start: 0.8972 (t0) cc_final: 0.8448 (t0) REVERT: D 260 MET cc_start: 0.9326 (mmp) cc_final: 0.8891 (mmm) REVERT: D 328 TYR cc_start: 0.9029 (t80) cc_final: 0.8792 (t80) REVERT: D 403 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7322 (tp30) REVERT: D 442 MET cc_start: 0.8144 (tmm) cc_final: 0.7781 (tmm) REVERT: D 497 MET cc_start: 0.9278 (ttt) cc_final: 0.8371 (tmm) REVERT: D 501 ILE cc_start: 0.9425 (pt) cc_final: 0.9005 (pt) REVERT: D 509 HIS cc_start: 0.9075 (t70) cc_final: 0.8653 (t70) REVERT: D 535 GLU cc_start: 0.8265 (tm-30) cc_final: 0.8014 (tm-30) REVERT: D 578 MET cc_start: 0.8793 (tmm) cc_final: 0.8296 (tmm) REVERT: D 587 GLN cc_start: 0.8988 (tp40) cc_final: 0.8587 (tp40) REVERT: D 596 GLN cc_start: 0.9374 (mm110) cc_final: 0.9146 (mm110) REVERT: D 603 MET cc_start: 0.8589 (ttt) cc_final: 0.8256 (tmm) REVERT: D 635 ASN cc_start: 0.9150 (t0) cc_final: 0.8942 (t0) REVERT: C 41 GLN cc_start: 0.9233 (mp10) cc_final: 0.9023 (mp10) REVERT: C 99 MET cc_start: 0.8574 (mpp) cc_final: 0.8250 (mpp) REVERT: C 132 LEU cc_start: 0.9380 (tp) cc_final: 0.9023 (pp) REVERT: C 310 GLN cc_start: 0.8795 (tp40) cc_final: 0.8445 (tp40) REVERT: C 328 TYR cc_start: 0.9172 (t80) cc_final: 0.8938 (t80) REVERT: C 403 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7402 (tp30) REVERT: C 442 MET cc_start: 0.7886 (tmm) cc_final: 0.7537 (tmm) REVERT: C 491 MET cc_start: 0.8206 (ttm) cc_final: 0.7742 (tmm) REVERT: C 497 MET cc_start: 0.9258 (ttt) cc_final: 0.8400 (tmm) REVERT: C 501 ILE cc_start: 0.9421 (pt) cc_final: 0.9006 (pt) REVERT: C 509 HIS cc_start: 0.9045 (t70) cc_final: 0.8644 (t70) REVERT: C 535 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8150 (tm-30) REVERT: C 572 ASN cc_start: 0.8020 (m110) cc_final: 0.7731 (m110) REVERT: C 603 MET cc_start: 0.8584 (ttt) cc_final: 0.8311 (tmm) REVERT: C 608 MET cc_start: 0.7863 (tpp) cc_final: 0.7657 (tpt) REVERT: C 635 ASN cc_start: 0.9149 (t0) cc_final: 0.8946 (t0) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.2698 time to fit residues: 208.4046 Evaluate side-chains 396 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 0.0970 chunk 67 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 142 optimal weight: 0.0970 chunk 152 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 203 optimal weight: 0.7980 chunk 214 optimal weight: 8.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19388 Z= 0.132 Angle : 0.686 9.516 26324 Z= 0.312 Chirality : 0.042 0.153 2984 Planarity : 0.003 0.047 3316 Dihedral : 5.645 49.170 2612 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.17), residues: 2340 helix: -1.13 (0.16), residues: 1020 sheet: 1.09 (0.65), residues: 56 loop : -1.73 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 286 HIS 0.003 0.000 HIS A 157 PHE 0.018 0.001 PHE C 574 TYR 0.019 0.001 TYR B 328 ARG 0.008 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 2.203 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: 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 126 MET cc_start: 0.9069 (ttm) cc_final: 0.8685 (ttm) REVERT: A 159 LEU cc_start: 0.7251 (tp) cc_final: 0.6936 (tt) REVERT: A 252 ASN cc_start: 0.8904 (t0) cc_final: 0.8356 (t0) REVERT: A 260 MET cc_start: 0.9352 (mmp) cc_final: 0.9041 (mmm) REVERT: A 309 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 403 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7349 (tp30) REVERT: A 442 MET cc_start: 0.8127 (tmm) cc_final: 0.7832 (tmm) REVERT: A 497 MET cc_start: 0.9284 (ttt) cc_final: 0.8339 (tmm) REVERT: A 501 ILE cc_start: 0.9439 (pt) cc_final: 0.9102 (pt) REVERT: A 509 HIS cc_start: 0.8998 (t70) cc_final: 0.8538 (t70) REVERT: A 535 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7848 (tm-30) REVERT: A 587 GLN cc_start: 0.9129 (tp40) cc_final: 0.8891 (tp40) REVERT: A 603 MET cc_start: 0.8518 (ttt) cc_final: 0.8269 (tmm) REVERT: B 99 MET cc_start: 0.8608 (mpp) cc_final: 0.8193 (mpp) REVERT: B 132 LEU cc_start: 0.9358 (tp) cc_final: 0.9020 (pp) REVERT: B 260 MET cc_start: 0.9227 (mmp) cc_final: 0.8903 (mmm) REVERT: B 403 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7406 (tp30) REVERT: B 442 MET cc_start: 0.7944 (tmm) cc_final: 0.7202 (tmm) REVERT: B 450 GLU cc_start: 0.7918 (mp0) cc_final: 0.7636 (mp0) REVERT: B 497 MET cc_start: 0.9266 (ttt) cc_final: 0.8318 (tmm) REVERT: B 501 ILE cc_start: 0.9406 (pt) cc_final: 0.8999 (pt) REVERT: B 509 HIS cc_start: 0.8995 (t70) cc_final: 0.8573 (t70) REVERT: B 535 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7902 (tm-30) REVERT: B 572 ASN cc_start: 0.7985 (m110) cc_final: 0.7759 (m110) REVERT: B 603 MET cc_start: 0.8582 (ttt) cc_final: 0.8312 (tmm) REVERT: D 59 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7326 (ttp80) REVERT: D 99 MET cc_start: 0.8532 (mpp) cc_final: 0.8200 (mpp) REVERT: D 132 LEU cc_start: 0.9352 (tp) cc_final: 0.9019 (pp) REVERT: D 252 ASN cc_start: 0.8914 (t0) cc_final: 0.8378 (t0) REVERT: D 328 TYR cc_start: 0.8993 (t80) cc_final: 0.8753 (t80) REVERT: D 403 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7340 (tp30) REVERT: D 442 MET cc_start: 0.8251 (tmm) cc_final: 0.7901 (tmm) REVERT: D 491 MET cc_start: 0.8283 (ttm) cc_final: 0.7872 (tmm) REVERT: D 497 MET cc_start: 0.9343 (ttt) cc_final: 0.8472 (tmm) REVERT: D 501 ILE cc_start: 0.9422 (pt) cc_final: 0.9020 (pt) REVERT: D 509 HIS cc_start: 0.9059 (t70) cc_final: 0.8629 (t70) REVERT: D 535 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7919 (tm-30) REVERT: D 578 MET cc_start: 0.8726 (tmm) cc_final: 0.8306 (tmm) REVERT: D 587 GLN cc_start: 0.9022 (tp40) cc_final: 0.8608 (tp40) REVERT: D 596 GLN cc_start: 0.9368 (mm110) cc_final: 0.9136 (mm110) REVERT: D 603 MET cc_start: 0.8564 (ttt) cc_final: 0.8223 (tmm) REVERT: D 635 ASN cc_start: 0.9137 (t0) cc_final: 0.8912 (t0) REVERT: C 41 GLN cc_start: 0.9252 (mp10) cc_final: 0.9047 (mp10) REVERT: C 99 MET cc_start: 0.8557 (mpp) cc_final: 0.8240 (mpp) REVERT: C 132 LEU cc_start: 0.9372 (tp) cc_final: 0.9022 (pp) REVERT: C 260 MET cc_start: 0.9152 (mmp) cc_final: 0.8772 (mmm) REVERT: C 310 GLN cc_start: 0.8798 (tp40) cc_final: 0.8405 (tp40) REVERT: C 403 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7400 (tp30) REVERT: C 442 MET cc_start: 0.7916 (tmm) cc_final: 0.7555 (tmm) REVERT: C 491 MET cc_start: 0.8353 (ttm) cc_final: 0.7951 (tmm) REVERT: C 497 MET cc_start: 0.9257 (ttt) cc_final: 0.8330 (tmm) REVERT: C 501 ILE cc_start: 0.9401 (pt) cc_final: 0.9007 (pt) REVERT: C 509 HIS cc_start: 0.8997 (t70) cc_final: 0.8587 (t70) REVERT: C 535 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 603 MET cc_start: 0.8533 (ttt) cc_final: 0.8274 (tmm) REVERT: C 635 ASN cc_start: 0.9269 (t0) cc_final: 0.9052 (t0) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.2686 time to fit residues: 209.9220 Evaluate side-chains 404 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 0.0370 chunk 63 optimal weight: 0.6980 chunk 188 optimal weight: 0.9980 chunk 197 optimal weight: 0.0670 chunk 207 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19388 Z= 0.134 Angle : 0.700 10.364 26324 Z= 0.317 Chirality : 0.042 0.152 2984 Planarity : 0.003 0.046 3316 Dihedral : 5.513 47.559 2612 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.17), residues: 2340 helix: -1.14 (0.16), residues: 1052 sheet: 1.19 (0.64), residues: 56 loop : -1.88 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 495 HIS 0.003 0.000 HIS C 84 PHE 0.016 0.001 PHE B 574 TYR 0.010 0.001 TYR C 415 ARG 0.008 0.000 ARG C 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 2.175 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8481 (mpp) cc_final: 0.8166 (mpp) REVERT: A 126 MET cc_start: 0.9120 (ttm) cc_final: 0.8735 (ttm) REVERT: A 159 LEU cc_start: 0.7212 (tp) cc_final: 0.6899 (tt) REVERT: A 252 ASN cc_start: 0.8877 (t0) cc_final: 0.8084 (t0) REVERT: A 260 MET cc_start: 0.9310 (mmp) cc_final: 0.8964 (mmm) REVERT: A 309 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 326 ARG cc_start: 0.8203 (mtp-110) cc_final: 0.7767 (mmm-85) REVERT: A 403 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7327 (tp30) REVERT: A 442 MET cc_start: 0.8118 (tmm) cc_final: 0.7815 (tmm) REVERT: A 497 MET cc_start: 0.9295 (ttt) cc_final: 0.8342 (tmm) REVERT: A 501 ILE cc_start: 0.9412 (pt) cc_final: 0.9095 (pt) REVERT: A 509 HIS cc_start: 0.9010 (t70) cc_final: 0.8559 (t70) REVERT: A 535 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 587 GLN cc_start: 0.9129 (tp40) cc_final: 0.8883 (tp40) REVERT: A 596 GLN cc_start: 0.9319 (mm110) cc_final: 0.9084 (mm110) REVERT: A 603 MET cc_start: 0.8497 (ttt) cc_final: 0.8257 (tmm) REVERT: B 38 MET cc_start: 0.8181 (pmm) cc_final: 0.7720 (pmm) REVERT: B 41 GLN cc_start: 0.9372 (mp10) cc_final: 0.9120 (mp10) REVERT: B 99 MET cc_start: 0.8598 (mpp) cc_final: 0.8178 (mpp) REVERT: B 132 LEU cc_start: 0.9358 (tp) cc_final: 0.9019 (pp) REVERT: B 260 MET cc_start: 0.9213 (mmp) cc_final: 0.8870 (mmm) REVERT: B 403 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7367 (tp30) REVERT: B 442 MET cc_start: 0.7951 (tmm) cc_final: 0.7436 (tmm) REVERT: B 497 MET cc_start: 0.9265 (ttt) cc_final: 0.8303 (tmm) REVERT: B 501 ILE cc_start: 0.9372 (pt) cc_final: 0.9016 (pt) REVERT: B 509 HIS cc_start: 0.8997 (t70) cc_final: 0.8584 (t70) REVERT: B 535 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 572 ASN cc_start: 0.8051 (m110) cc_final: 0.7785 (m110) REVERT: B 603 MET cc_start: 0.8623 (ttt) cc_final: 0.8333 (tmm) REVERT: D 59 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7354 (ttp80) REVERT: D 99 MET cc_start: 0.8545 (mpp) cc_final: 0.8206 (mpp) REVERT: D 132 LEU cc_start: 0.9373 (tp) cc_final: 0.9048 (pp) REVERT: D 252 ASN cc_start: 0.8885 (t0) cc_final: 0.8324 (t0) REVERT: D 260 MET cc_start: 0.9132 (mmp) cc_final: 0.8882 (mmm) REVERT: D 328 TYR cc_start: 0.9087 (t80) cc_final: 0.8799 (t80) REVERT: D 403 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7339 (tp30) REVERT: D 442 MET cc_start: 0.8250 (tmm) cc_final: 0.7918 (tmm) REVERT: D 491 MET cc_start: 0.8450 (ttm) cc_final: 0.8013 (tmm) REVERT: D 497 MET cc_start: 0.9331 (ttt) cc_final: 0.8501 (tmm) REVERT: D 501 ILE cc_start: 0.9402 (pt) cc_final: 0.9022 (pt) REVERT: D 509 HIS cc_start: 0.9025 (t70) cc_final: 0.8581 (t70) REVERT: D 535 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7914 (tm-30) REVERT: D 587 GLN cc_start: 0.9032 (tp40) cc_final: 0.8617 (tp40) REVERT: D 596 GLN cc_start: 0.9347 (mm110) cc_final: 0.9099 (mm110) REVERT: D 603 MET cc_start: 0.8576 (ttt) cc_final: 0.8232 (tmm) REVERT: C 38 MET cc_start: 0.8251 (pmm) cc_final: 0.8043 (pmm) REVERT: C 41 GLN cc_start: 0.9256 (mp10) cc_final: 0.9043 (mp10) REVERT: C 99 MET cc_start: 0.8515 (mpp) cc_final: 0.8218 (mpp) REVERT: C 132 LEU cc_start: 0.9393 (tp) cc_final: 0.9066 (pp) REVERT: C 260 MET cc_start: 0.9123 (mmp) cc_final: 0.8828 (mmm) REVERT: C 310 GLN cc_start: 0.8750 (tp40) cc_final: 0.8438 (tp40) REVERT: C 403 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7349 (tp30) REVERT: C 442 MET cc_start: 0.7939 (tmm) cc_final: 0.7592 (tmm) REVERT: C 491 MET cc_start: 0.8361 (ttm) cc_final: 0.7962 (tmm) REVERT: C 497 MET cc_start: 0.9247 (ttt) cc_final: 0.8328 (tmm) REVERT: C 501 ILE cc_start: 0.9373 (pt) cc_final: 0.9008 (pt) REVERT: C 509 HIS cc_start: 0.8996 (t70) cc_final: 0.8588 (t70) REVERT: C 535 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8107 (tm-30) REVERT: C 536 LEU cc_start: 0.7990 (tt) cc_final: 0.7787 (tt) REVERT: C 572 ASN cc_start: 0.8037 (m110) cc_final: 0.7720 (m110) REVERT: C 603 MET cc_start: 0.8524 (ttt) cc_final: 0.8264 (tmm) REVERT: C 635 ASN cc_start: 0.9294 (t0) cc_final: 0.9094 (t0) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.2617 time to fit residues: 205.6460 Evaluate side-chains 398 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 212 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 112 optimal weight: 0.0470 chunk 146 optimal weight: 4.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19388 Z= 0.145 Angle : 0.692 9.301 26324 Z= 0.317 Chirality : 0.042 0.150 2984 Planarity : 0.003 0.046 3316 Dihedral : 5.512 46.338 2612 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2340 helix: -0.80 (0.17), residues: 976 sheet: 1.10 (0.63), residues: 56 loop : -1.61 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 593 HIS 0.004 0.001 HIS A 84 PHE 0.024 0.001 PHE C 574 TYR 0.020 0.001 TYR B 328 ARG 0.008 0.000 ARG C 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 2.324 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.9102 (ttm) cc_final: 0.8716 (ttm) REVERT: A 159 LEU cc_start: 0.7375 (tp) cc_final: 0.7049 (tt) REVERT: A 252 ASN cc_start: 0.8948 (t0) cc_final: 0.8190 (t0) REVERT: A 260 MET cc_start: 0.9284 (mmp) cc_final: 0.9047 (mmm) REVERT: A 309 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8399 (tm-30) REVERT: A 403 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7424 (tp30) REVERT: A 442 MET cc_start: 0.8034 (tmm) cc_final: 0.7685 (tmm) REVERT: A 497 MET cc_start: 0.9299 (ttt) cc_final: 0.8395 (tmm) REVERT: A 501 ILE cc_start: 0.9457 (pt) cc_final: 0.9085 (pt) REVERT: A 509 HIS cc_start: 0.9028 (t70) cc_final: 0.8582 (t70) REVERT: A 535 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7888 (tm-30) REVERT: A 587 GLN cc_start: 0.9119 (tp40) cc_final: 0.8914 (tp40) REVERT: A 596 GLN cc_start: 0.9333 (mm110) cc_final: 0.9095 (mm110) REVERT: A 603 MET cc_start: 0.8556 (ttt) cc_final: 0.8287 (tmm) REVERT: B 99 MET cc_start: 0.8585 (mpp) cc_final: 0.8194 (mpp) REVERT: B 132 LEU cc_start: 0.9400 (tp) cc_final: 0.9046 (pp) REVERT: B 260 MET cc_start: 0.9231 (mmp) cc_final: 0.8866 (mmm) REVERT: B 403 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7423 (tp30) REVERT: B 497 MET cc_start: 0.9289 (ttt) cc_final: 0.8294 (tmm) REVERT: B 501 ILE cc_start: 0.9404 (pt) cc_final: 0.9039 (pt) REVERT: B 509 HIS cc_start: 0.9013 (t70) cc_final: 0.8603 (t70) REVERT: B 535 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7841 (tm-30) REVERT: B 572 ASN cc_start: 0.8088 (m110) cc_final: 0.7755 (m110) REVERT: B 603 MET cc_start: 0.8650 (ttt) cc_final: 0.8336 (tmm) REVERT: D 59 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7386 (ttp80) REVERT: D 99 MET cc_start: 0.8542 (mpp) cc_final: 0.8230 (mpp) REVERT: D 132 LEU cc_start: 0.9410 (tp) cc_final: 0.9068 (pp) REVERT: D 252 ASN cc_start: 0.8920 (t0) cc_final: 0.8365 (t0) REVERT: D 260 MET cc_start: 0.9136 (mmp) cc_final: 0.8862 (mmm) REVERT: D 328 TYR cc_start: 0.9050 (t80) cc_final: 0.8835 (t80) REVERT: D 403 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7394 (tp30) REVERT: D 442 MET cc_start: 0.8097 (tmm) cc_final: 0.7690 (tmm) REVERT: D 491 MET cc_start: 0.8337 (ttm) cc_final: 0.7951 (tmm) REVERT: D 497 MET cc_start: 0.9350 (ttt) cc_final: 0.8509 (tmm) REVERT: D 501 ILE cc_start: 0.9428 (pt) cc_final: 0.9051 (pt) REVERT: D 509 HIS cc_start: 0.9026 (t70) cc_final: 0.8575 (t70) REVERT: D 535 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7902 (tm-30) REVERT: D 587 GLN cc_start: 0.8970 (tp40) cc_final: 0.8504 (tp40) REVERT: D 596 GLN cc_start: 0.9356 (mm110) cc_final: 0.9111 (mm110) REVERT: D 603 MET cc_start: 0.8599 (ttt) cc_final: 0.8251 (tmm) REVERT: D 635 ASN cc_start: 0.9141 (t0) cc_final: 0.8914 (t0) REVERT: C 38 MET cc_start: 0.8277 (pmm) cc_final: 0.8051 (pmm) REVERT: C 41 GLN cc_start: 0.9260 (mp10) cc_final: 0.9055 (mp10) REVERT: C 99 MET cc_start: 0.8478 (mpp) cc_final: 0.8200 (mpp) REVERT: C 132 LEU cc_start: 0.9430 (tp) cc_final: 0.9088 (pp) REVERT: C 260 MET cc_start: 0.9140 (mmp) cc_final: 0.8799 (mmm) REVERT: C 309 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8218 (tm-30) REVERT: C 310 GLN cc_start: 0.8779 (tp40) cc_final: 0.8464 (tp40) REVERT: C 403 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7402 (tp30) REVERT: C 497 MET cc_start: 0.9272 (ttt) cc_final: 0.8314 (tmm) REVERT: C 501 ILE cc_start: 0.9411 (pt) cc_final: 0.9040 (pt) REVERT: C 509 HIS cc_start: 0.8992 (t70) cc_final: 0.8585 (t70) REVERT: C 535 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 603 MET cc_start: 0.8671 (ttt) cc_final: 0.8364 (tmm) REVERT: C 635 ASN cc_start: 0.9296 (t0) cc_final: 0.9083 (t0) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.2591 time to fit residues: 199.3597 Evaluate side-chains 388 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 0.0040 chunk 161 optimal weight: 6.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.101862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.081983 restraints weight = 53093.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.084757 restraints weight = 34515.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.086817 restraints weight = 24690.807| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19388 Z= 0.138 Angle : 0.692 9.948 26324 Z= 0.315 Chirality : 0.042 0.149 2984 Planarity : 0.003 0.046 3316 Dihedral : 5.393 44.845 2612 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 2340 helix: -0.74 (0.17), residues: 952 sheet: 1.13 (0.62), residues: 56 loop : -1.53 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 613 HIS 0.003 0.000 HIS A 157 PHE 0.024 0.001 PHE C 574 TYR 0.027 0.001 TYR C 328 ARG 0.007 0.000 ARG C 409 =============================================================================== Job complete usr+sys time: 4187.41 seconds wall clock time: 77 minutes 5.87 seconds (4625.87 seconds total)