Starting phenix.real_space_refine on Tue Mar 19 15:45:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/03_2024/6ip2_9698_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/03_2024/6ip2_9698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/03_2024/6ip2_9698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/03_2024/6ip2_9698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/03_2024/6ip2_9698_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/03_2024/6ip2_9698_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 138 5.16 5 C 15486 2.51 5 N 4302 2.21 5 O 4698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 24660 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 11, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 486} Chain: "C" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 493} Chain: "D" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 493} Chain: "E" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 492} Chain: "F" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 6, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 491} Chain: "A" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 493} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.03, per 1000 atoms: 0.57 Number of scatterers: 24660 At special positions: 0 Unit cell: (143.719, 141.106, 112.362, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 36 15.00 O 4698 8.00 N 4302 7.00 C 15486 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: 9.26 Conformation dependent library (CDL) restraints added in 4.1 seconds 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5772 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 15 sheets defined 35.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.836A pdb=" N PHE B 227 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N SER B 228 " --> pdb=" O LYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.520A pdb=" N GLN B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 299 through 302 No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.656A pdb=" N SER B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.817A pdb=" N HIS B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 removed outlier: 4.178A pdb=" N VAL B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 432 " --> pdb=" O GLU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 454 removed outlier: 3.560A pdb=" N GLY B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 removed outlier: 3.613A pdb=" N ALA B 482 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 530 removed outlier: 4.659A pdb=" N ASP B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 558 removed outlier: 3.540A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 592 removed outlier: 4.091A pdb=" N LYS B 587 " --> pdb=" O GLN B 583 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 589 " --> pdb=" O MET B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 608 No H-bonds generated for 'chain 'B' and resid 605 through 608' Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 649 through 654 removed outlier: 3.743A pdb=" N GLU B 654 " --> pdb=" O ASP B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 683 removed outlier: 3.987A pdb=" N LEU B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 removed outlier: 3.762A pdb=" N GLN B 697 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 718 removed outlier: 3.771A pdb=" N GLU B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 729 No H-bonds generated for 'chain 'B' and resid 726 through 729' Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 231 through 234 No H-bonds generated for 'chain 'C' and resid 231 through 234' Processing helix chain 'C' and resid 244 through 247 No H-bonds generated for 'chain 'C' and resid 244 through 247' Processing helix chain 'C' and resid 268 through 271 No H-bonds generated for 'chain 'C' and resid 268 through 271' Processing helix chain 'C' and resid 289 through 292 removed outlier: 4.057A pdb=" N ASN C 292 " --> pdb=" O GLU C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 297 through 304 removed outlier: 3.741A pdb=" N ALA C 300 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 301 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG C 303 " --> pdb=" O ALA C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 4.232A pdb=" N GLU C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.661A pdb=" N LEU C 354 " --> pdb=" O VAL C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 354' Processing helix chain 'C' and resid 400 through 413 removed outlier: 4.097A pdb=" N LEU C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 412 " --> pdb=" O HIS C 408 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 removed outlier: 4.042A pdb=" N VAL C 431 " --> pdb=" O LYS C 427 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 432 " --> pdb=" O GLU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 456 removed outlier: 3.535A pdb=" N GLY C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 480 No H-bonds generated for 'chain 'C' and resid 477 through 480' Processing helix chain 'C' and resid 512 through 530 removed outlier: 4.552A pdb=" N VAL C 517 " --> pdb=" O PRO C 513 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 520 " --> pdb=" O ARG C 516 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 removed outlier: 3.574A pdb=" N SER C 560 " --> pdb=" O ILE C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 578 through 592 removed outlier: 3.882A pdb=" N CYS C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 608 No H-bonds generated for 'chain 'C' and resid 605 through 608' Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 649 through 654 Processing helix chain 'C' and resid 673 through 683 removed outlier: 3.524A pdb=" N LEU C 682 " --> pdb=" O GLU C 678 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'C' and resid 707 through 718 removed outlier: 3.739A pdb=" N GLU C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 734 removed outlier: 4.334A pdb=" N ALA C 731 " --> pdb=" O ARG C 727 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG C 734 " --> pdb=" O LEU C 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 241 through 243 No H-bonds generated for 'chain 'D' and resid 241 through 243' Processing helix chain 'D' and resid 245 through 248 No H-bonds generated for 'chain 'D' and resid 245 through 248' Processing helix chain 'D' and resid 266 through 272 removed outlier: 3.694A pdb=" N ALA D 270 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 3.774A pdb=" N ASN D 301 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG D 303 " --> pdb=" O ALA D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 298 through 303' Processing helix chain 'D' and resid 307 through 313 removed outlier: 3.636A pdb=" N GLU D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 307 through 313' Processing helix chain 'D' and resid 349 through 352 No H-bonds generated for 'chain 'D' and resid 349 through 352' Processing helix chain 'D' and resid 376 through 378 No H-bonds generated for 'chain 'D' and resid 376 through 378' Processing helix chain 'D' and resid 381 through 383 No H-bonds generated for 'chain 'D' and resid 381 through 383' Processing helix chain 'D' and resid 400 through 410 removed outlier: 3.797A pdb=" N LEU D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 431 No H-bonds generated for 'chain 'D' and resid 428 through 431' Processing helix chain 'D' and resid 438 through 454 removed outlier: 3.601A pdb=" N ASN D 454 " --> pdb=" O SER D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 483 Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 512 through 529 removed outlier: 4.084A pdb=" N VAL D 517 " --> pdb=" O PRO D 513 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP D 520 " --> pdb=" O ARG D 516 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 524 " --> pdb=" O ASP D 520 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 558 Processing helix chain 'D' and resid 570 through 573 Processing helix chain 'D' and resid 578 through 591 removed outlier: 3.800A pdb=" N CYS D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 584 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 587 " --> pdb=" O GLN D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 608 No H-bonds generated for 'chain 'D' and resid 605 through 608' Processing helix chain 'D' and resid 620 through 623 No H-bonds generated for 'chain 'D' and resid 620 through 623' Processing helix chain 'D' and resid 649 through 652 No H-bonds generated for 'chain 'D' and resid 649 through 652' Processing helix chain 'D' and resid 673 through 683 removed outlier: 3.523A pdb=" N LEU D 683 " --> pdb=" O ALA D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 698 removed outlier: 3.535A pdb=" N THR D 693 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 694 " --> pdb=" O GLU D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 717 Processing helix chain 'D' and resid 727 through 734 removed outlier: 3.911A pdb=" N ARG D 734 " --> pdb=" O LEU D 730 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 227 No H-bonds generated for 'chain 'E' and resid 224 through 227' Processing helix chain 'E' and resid 229 through 233 removed outlier: 3.564A pdb=" N ARG E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 229 through 233' Processing helix chain 'E' and resid 243 through 247 Processing helix chain 'E' and resid 266 through 272 removed outlier: 3.537A pdb=" N ALA E 270 " --> pdb=" O LYS E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 307 through 312 Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 348 through 358 removed outlier: 3.673A pdb=" N ASN E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE E 358 " --> pdb=" O LEU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 410 removed outlier: 3.549A pdb=" N ILE E 406 " --> pdb=" O GLY E 402 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE E 409 " --> pdb=" O GLN E 405 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS E 410 " --> pdb=" O ILE E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 432 Processing helix chain 'E' and resid 438 through 454 removed outlier: 3.686A pdb=" N VAL E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA E 447 " --> pdb=" O GLY E 443 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER E 450 " --> pdb=" O ARG E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 483 removed outlier: 3.572A pdb=" N ALA E 482 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 501 No H-bonds generated for 'chain 'E' and resid 499 through 501' Processing helix chain 'E' and resid 512 through 530 removed outlier: 3.765A pdb=" N ARG E 516 " --> pdb=" O ASP E 512 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP E 520 " --> pdb=" O ARG E 516 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 522 " --> pdb=" O LEU E 518 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 526 " --> pdb=" O GLU E 522 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN E 527 " --> pdb=" O LEU E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 559 Processing helix chain 'E' and resid 570 through 572 No H-bonds generated for 'chain 'E' and resid 570 through 572' Processing helix chain 'E' and resid 580 through 591 removed outlier: 4.127A pdb=" N ILE E 588 " --> pdb=" O ALA E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 608 No H-bonds generated for 'chain 'E' and resid 605 through 608' Processing helix chain 'E' and resid 620 through 623 No H-bonds generated for 'chain 'E' and resid 620 through 623' Processing helix chain 'E' and resid 649 through 654 Processing helix chain 'E' and resid 673 through 681 Processing helix chain 'E' and resid 688 through 698 Processing helix chain 'E' and resid 707 through 717 removed outlier: 3.550A pdb=" N ILE E 714 " --> pdb=" O LEU E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 732 Processing helix chain 'F' and resid 267 through 275 removed outlier: 3.824A pdb=" N GLN F 272 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 330 through 333 No H-bonds generated for 'chain 'F' and resid 330 through 333' Processing helix chain 'F' and resid 346 through 349 Processing helix chain 'F' and resid 351 through 354 No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 400 through 413 removed outlier: 3.837A pdb=" N ILE F 406 " --> pdb=" O GLY F 402 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG F 413 " --> pdb=" O ILE F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 430 Processing helix chain 'F' and resid 438 through 455 Processing helix chain 'F' and resid 499 through 502 No H-bonds generated for 'chain 'F' and resid 499 through 502' Processing helix chain 'F' and resid 512 through 529 removed outlier: 3.779A pdb=" N ASP F 520 " --> pdb=" O ARG F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 560 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 578 through 591 removed outlier: 3.503A pdb=" N MET F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE F 588 " --> pdb=" O ALA F 584 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 591 " --> pdb=" O LYS F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 608 No H-bonds generated for 'chain 'F' and resid 605 through 608' Processing helix chain 'F' and resid 620 through 627 Processing helix chain 'F' and resid 649 through 654 Processing helix chain 'F' and resid 673 through 681 Processing helix chain 'F' and resid 688 through 698 removed outlier: 3.708A pdb=" N VAL F 698 " --> pdb=" O ILE F 694 " (cutoff:3.500A) Processing helix chain 'F' and resid 707 through 718 Processing helix chain 'F' and resid 725 through 732 Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.307A pdb=" N ILE A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 273 Processing helix chain 'A' and resid 288 through 291 removed outlier: 3.574A pdb=" N LEU A 291 " --> pdb=" O PRO A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.535A pdb=" N LEU A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.529A pdb=" N ILE A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 438 through 456 removed outlier: 3.730A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 501 No H-bonds generated for 'chain 'A' and resid 499 through 501' Processing helix chain 'A' and resid 512 through 530 removed outlier: 3.765A pdb=" N LEU A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.551A pdb=" N ALA A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 578 through 591 Processing helix chain 'A' and resid 605 through 608 No H-bonds generated for 'chain 'A' and resid 605 through 608' Processing helix chain 'A' and resid 620 through 629 removed outlier: 3.543A pdb=" N LEU A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.640A pdb=" N LEU A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.809A pdb=" N GLN A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.642A pdb=" N LEU A 711 " --> pdb=" O ILE A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 Processing sheet with id= A, first strand: chain 'B' and resid 391 through 393 removed outlier: 3.899A pdb=" N VAL B 391 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 369 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU B 258 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY B 371 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 372 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 663 through 667 removed outlier: 3.637A pdb=" N THR B 663 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU B 640 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL B 539 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 642 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU B 541 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY B 644 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLY B 543 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR B 646 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 645 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE B 564 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL B 601 " --> pdb=" O PHE B 564 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS B 566 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 391 through 393 removed outlier: 4.075A pdb=" N VAL C 391 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL C 369 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU C 258 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY C 371 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS C 283 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 663 through 667 removed outlier: 3.721A pdb=" N THR C 663 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 640 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL C 539 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE C 642 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU C 541 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY C 644 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLY C 543 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR C 646 " --> pdb=" O GLY C 543 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER C 598 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE C 643 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 600 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N THR C 645 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL C 602 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE C 564 " --> pdb=" O CYS C 599 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL C 601 " --> pdb=" O PHE C 564 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LYS C 566 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 256 through 258 removed outlier: 6.285A pdb=" N VAL D 391 " --> pdb=" O LEU D 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 282 through 284 removed outlier: 6.808A pdb=" N ILE D 324 " --> pdb=" O LYS D 283 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 663 through 667 removed outlier: 3.789A pdb=" N THR D 663 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU D 640 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL D 539 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 642 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU D 541 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLY D 644 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLY D 543 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 645 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE D 564 " --> pdb=" O CYS D 599 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL D 601 " --> pdb=" O PHE D 564 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS D 566 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 256 through 258 removed outlier: 6.256A pdb=" N VAL E 391 " --> pdb=" O LEU E 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'E' and resid 324 through 327 removed outlier: 5.929A pdb=" N LEU E 368 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE E 327 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE E 370 " --> pdb=" O PHE E 327 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 663 through 667 removed outlier: 3.721A pdb=" N THR E 663 " --> pdb=" O SER E 538 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU E 640 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL E 539 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE E 642 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU E 541 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY E 644 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY E 543 " --> pdb=" O GLY E 644 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 255 through 258 removed outlier: 5.571A pdb=" N VAL F 369 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU F 258 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY F 371 " --> pdb=" O LEU F 258 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 283 through 285 Processing sheet with id= M, first strand: chain 'F' and resid 663 through 665 removed outlier: 3.595A pdb=" N THR F 663 " --> pdb=" O SER F 538 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU F 640 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL F 539 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE F 642 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU F 541 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY F 644 " --> pdb=" O LEU F 541 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE F 564 " --> pdb=" O CYS F 599 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL F 601 " --> pdb=" O PHE F 564 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS F 566 " --> pdb=" O VAL F 601 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 255 through 258 removed outlier: 5.780A pdb=" N VAL A 369 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU A 258 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY A 371 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 327 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 372 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 283 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 663 through 666 removed outlier: 6.672A pdb=" N LEU A 640 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 539 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE A 642 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU A 541 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY A 644 " --> pdb=" O LEU A 541 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1533 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: 6.60 Time building geometry restraints manager: 10.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7206 1.33 - 1.45: 3428 1.45 - 1.57: 14098 1.57 - 1.69: 60 1.69 - 1.81: 240 Bond restraints: 25032 Sorted by residual: bond pdb=" C4 ATP F 801 " pdb=" C5 ATP F 801 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.79e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.62e+01 bond pdb=" C4 ATP F 802 " pdb=" C5 ATP F 802 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.44e+01 bond pdb=" C4 ATP E 801 " pdb=" C5 ATP E 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C4 ATP E 802 " pdb=" C5 ATP E 802 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.16e+01 ... (remaining 25027 not shown) Histogram of bond angle deviations from ideal: 97.60 - 107.03: 981 107.03 - 116.47: 16486 116.47 - 125.91: 15953 125.91 - 135.34: 355 135.34 - 144.78: 23 Bond angle restraints: 33798 Sorted by residual: angle pdb=" PB ATP D 802 " pdb=" O3B ATP D 802 " pdb=" PG ATP D 802 " ideal model delta sigma weight residual 139.87 116.98 22.89 1.00e+00 1.00e+00 5.24e+02 angle pdb=" PB ATP F 802 " pdb=" O3B ATP F 802 " pdb=" PG ATP F 802 " ideal model delta sigma weight residual 139.87 117.75 22.12 1.00e+00 1.00e+00 4.89e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 118.33 21.54 1.00e+00 1.00e+00 4.64e+02 angle pdb=" PB ATP C 802 " pdb=" O3B ATP C 802 " pdb=" PG ATP C 802 " ideal model delta sigma weight residual 139.87 118.51 21.36 1.00e+00 1.00e+00 4.56e+02 angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 119.18 20.69 1.00e+00 1.00e+00 4.28e+02 ... (remaining 33793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.65: 15199 26.65 - 53.31: 479 53.31 - 79.96: 56 79.96 - 106.61: 9 106.61 - 133.27: 1 Dihedral angle restraints: 15744 sinusoidal: 6816 harmonic: 8928 Sorted by residual: dihedral pdb=" CA HIS B 417 " pdb=" C HIS B 417 " pdb=" N GLN B 418 " pdb=" CA GLN B 418 " ideal model delta harmonic sigma weight residual 180.00 46.73 133.27 0 5.00e+00 4.00e-02 7.10e+02 dihedral pdb=" CA GLY D 615 " pdb=" C GLY D 615 " pdb=" N PRO D 616 " pdb=" CA PRO D 616 " ideal model delta harmonic sigma weight residual 180.00 -130.37 -49.63 0 5.00e+00 4.00e-02 9.85e+01 dihedral pdb=" CA LYS D 462 " pdb=" C LYS D 462 " pdb=" N VAL D 463 " pdb=" CA VAL D 463 " ideal model delta harmonic sigma weight residual -180.00 -132.29 -47.71 0 5.00e+00 4.00e-02 9.11e+01 ... (remaining 15741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2940 0.067 - 0.133: 798 0.133 - 0.200: 113 0.200 - 0.267: 22 0.267 - 0.333: 3 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CB ILE C 302 " pdb=" CA ILE C 302 " pdb=" CG1 ILE C 302 " pdb=" CG2 ILE C 302 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB THR B 494 " pdb=" CA THR B 494 " pdb=" OG1 THR B 494 " pdb=" CG2 THR B 494 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CG LEU D 473 " pdb=" CB LEU D 473 " pdb=" CD1 LEU D 473 " pdb=" CD2 LEU D 473 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 3873 not shown) Planarity restraints: 4308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 489 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO B 490 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 287 " -0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO C 288 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 288 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 288 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 287 " -0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO E 288 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 288 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 288 " -0.045 5.00e-02 4.00e+02 ... (remaining 4305 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4593 2.77 - 3.30: 23527 3.30 - 3.83: 39912 3.83 - 4.37: 48957 4.37 - 4.90: 78673 Nonbonded interactions: 195662 Sorted by model distance: nonbonded pdb=" OG SER A 421 " pdb=" OD1 ASP A 423 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR C 267 " pdb=" O3G ATP C 801 " model vdw 2.245 2.440 nonbonded pdb=" OE2 GLU D 468 " pdb=" OG SER D 472 " model vdw 2.278 2.440 nonbonded pdb=" O ARG C 232 " pdb=" OG SER D 450 " model vdw 2.281 2.440 nonbonded pdb=" OG SER F 569 " pdb=" OD1 ASP F 571 " model vdw 2.300 2.440 ... (remaining 195657 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.150 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: 0.010 Extract box with map and model: 2.510 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 65.040 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 0.082 25032 Z= 0.505 Angle : 1.380 22.891 33798 Z= 0.896 Chirality : 0.061 0.333 3876 Planarity : 0.008 0.127 4308 Dihedral : 12.869 133.268 9972 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.19 % Favored : 87.68 % Rotamer: Outliers : 0.26 % Allowed : 2.97 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.11 % Twisted Proline : 3.03 % Twisted General : 0.77 % 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: -5.47 (0.11), residues: 3108 helix: -4.28 (0.07), residues: 1294 sheet: -2.35 (0.26), residues: 355 loop : -3.26 (0.14), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 510 HIS 0.014 0.002 HIS A 417 PHE 0.025 0.003 PHE C 436 TYR 0.024 0.002 TYR F 259 ARG 0.008 0.001 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 861 time to evaluate : 2.808 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: B 256 ILE cc_start: 0.8943 (mt) cc_final: 0.8614 (mt) REVERT: B 285 VAL cc_start: 0.9367 (p) cc_final: 0.9089 (t) REVERT: B 510 TRP cc_start: 0.8092 (p-90) cc_final: 0.7891 (p90) REVERT: B 649 LYS cc_start: 0.8442 (tttp) cc_final: 0.8229 (ttpt) REVERT: C 268 LEU cc_start: 0.9087 (tp) cc_final: 0.8632 (tp) REVERT: C 283 LYS cc_start: 0.8373 (mmmt) cc_final: 0.7819 (mttp) REVERT: C 284 VAL cc_start: 0.9194 (t) cc_final: 0.8986 (p) REVERT: C 435 ASN cc_start: 0.8577 (t0) cc_final: 0.8063 (t0) REVERT: D 273 ILE cc_start: 0.9083 (tp) cc_final: 0.8877 (tt) REVERT: D 390 GLU cc_start: 0.7356 (tp30) cc_final: 0.7010 (mt-10) REVERT: D 397 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8748 (pt) REVERT: D 649 LYS cc_start: 0.8644 (tttm) cc_final: 0.8163 (ttpt) REVERT: E 312 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7041 (tm-30) REVERT: E 362 GLU cc_start: 0.7309 (pm20) cc_final: 0.7047 (tp30) REVERT: E 496 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5644 (tm-30) REVERT: E 498 ASP cc_start: 0.6172 (m-30) cc_final: 0.5881 (m-30) REVERT: E 542 GLU cc_start: 0.7780 (pt0) cc_final: 0.7469 (pt0) REVERT: E 561 ASN cc_start: 0.7882 (m110) cc_final: 0.7608 (t0) REVERT: E 624 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8022 (mm-40) REVERT: E 721 ASP cc_start: 0.7427 (m-30) cc_final: 0.7224 (m-30) REVERT: E 727 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7343 (ttm110) REVERT: F 322 LEU cc_start: 0.6394 (tp) cc_final: 0.6085 (tt) REVERT: F 340 MET cc_start: 0.5259 (ptm) cc_final: 0.3820 (mmt) REVERT: F 496 GLN cc_start: 0.4546 (tt0) cc_final: 0.4256 (mp10) REVERT: F 607 ARG cc_start: 0.8117 (mmt-90) cc_final: 0.7836 (tpp-160) REVERT: F 651 VAL cc_start: 0.8898 (t) cc_final: 0.8661 (p) REVERT: F 655 MET cc_start: 0.8122 (mtm) cc_final: 0.7906 (mtm) REVERT: A 233 ARG cc_start: 0.7429 (mtt90) cc_final: 0.6787 (mmm160) REVERT: A 276 MET cc_start: 0.6921 (mmm) cc_final: 0.6216 (mtp) REVERT: A 368 LEU cc_start: 0.7477 (tp) cc_final: 0.7226 (mp) REVERT: A 446 ARG cc_start: 0.8482 (tpp80) cc_final: 0.8000 (tpp-160) REVERT: A 467 MET cc_start: 0.0346 (mtm) cc_final: -0.0567 (mmt) REVERT: A 523 LEU cc_start: 0.8269 (mt) cc_final: 0.7883 (mt) REVERT: A 527 GLN cc_start: 0.7716 (tt0) cc_final: 0.7480 (tt0) REVERT: A 567 ILE cc_start: 0.8697 (mt) cc_final: 0.8305 (tt) REVERT: A 621 LEU cc_start: 0.8729 (tp) cc_final: 0.8407 (mt) outliers start: 7 outliers final: 3 residues processed: 867 average time/residue: 0.4230 time to fit residues: 538.8791 Evaluate side-chains 475 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 471 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN B 505 ASN B 530 ASN B 546 HIS ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN D 252 HIS ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN E 505 ASN E 546 HIS E 659 ASN F 417 HIS ** F 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 ASN F 526 GLN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS A 319 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN A 505 ASN A 653 GLN A 659 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25032 Z= 0.318 Angle : 0.828 13.050 33798 Z= 0.434 Chirality : 0.050 0.268 3876 Planarity : 0.006 0.123 4308 Dihedral : 12.897 89.129 3737 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.23 % Favored : 88.64 % Rotamer: Outliers : 3.72 % Allowed : 11.49 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.11 % Twisted Proline : 3.03 % Twisted General : 0.44 % 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: -4.33 (0.13), residues: 3108 helix: -2.97 (0.11), residues: 1341 sheet: -1.96 (0.27), residues: 349 loop : -2.93 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 510 HIS 0.012 0.002 HIS B 417 PHE 0.028 0.002 PHE B 436 TYR 0.012 0.002 TYR C 499 ARG 0.006 0.001 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 522 time to evaluate : 3.236 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: B 256 ILE cc_start: 0.8932 (mt) cc_final: 0.8664 (mt) REVERT: B 329 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6459 (mp0) REVERT: C 276 MET cc_start: 0.6111 (tpt) cc_final: 0.5639 (tpt) REVERT: C 283 LYS cc_start: 0.8384 (mmmt) cc_final: 0.7866 (mttp) REVERT: C 328 ASP cc_start: 0.8411 (t0) cc_final: 0.7730 (t0) REVERT: C 340 MET cc_start: 0.3908 (ptm) cc_final: 0.3669 (ptm) REVERT: C 435 ASN cc_start: 0.8571 (t0) cc_final: 0.8091 (t0) REVERT: C 682 LEU cc_start: 0.8707 (mt) cc_final: 0.8276 (mt) REVERT: D 248 MET cc_start: 0.4135 (mpp) cc_final: 0.3227 (mmm) REVERT: D 276 MET cc_start: 0.6432 (tpt) cc_final: 0.6158 (tpt) REVERT: D 390 GLU cc_start: 0.7294 (tp30) cc_final: 0.6353 (tp30) REVERT: D 469 LYS cc_start: 0.6217 (pttp) cc_final: 0.5956 (pttp) REVERT: D 678 GLU cc_start: 0.8082 (tp30) cc_final: 0.7869 (tp30) REVERT: D 712 MET cc_start: 0.8776 (tpp) cc_final: 0.8535 (tpp) REVERT: E 312 GLU cc_start: 0.7785 (mm-30) cc_final: 0.6767 (tm-30) REVERT: E 403 ARG cc_start: 0.8172 (mtm-85) cc_final: 0.7712 (mtm110) REVERT: E 498 ASP cc_start: 0.6501 (m-30) cc_final: 0.5902 (m-30) REVERT: E 561 ASN cc_start: 0.7926 (m110) cc_final: 0.7559 (t0) REVERT: E 590 ASP cc_start: 0.8558 (t0) cc_final: 0.8353 (t70) REVERT: E 624 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8129 (mm-40) REVERT: E 657 MET cc_start: 0.8098 (ttp) cc_final: 0.7793 (ttp) REVERT: E 712 MET cc_start: 0.7406 (mmm) cc_final: 0.7019 (mtt) REVERT: E 727 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7117 (ttm110) REVERT: F 248 MET cc_start: 0.5957 (ptt) cc_final: 0.5749 (tmm) REVERT: F 340 MET cc_start: 0.5250 (ptm) cc_final: 0.3606 (mmt) REVERT: F 410 HIS cc_start: 0.7914 (m90) cc_final: 0.7394 (m-70) REVERT: F 414 MET cc_start: 0.8070 (ttp) cc_final: 0.7728 (tpt) REVERT: F 496 GLN cc_start: 0.4532 (tt0) cc_final: 0.4091 (mp10) REVERT: F 499 TYR cc_start: 0.6994 (p90) cc_final: 0.6676 (p90) REVERT: F 712 MET cc_start: 0.8365 (mmm) cc_final: 0.7993 (mmm) REVERT: F 716 MET cc_start: 0.8465 (mtp) cc_final: 0.7612 (mpp) REVERT: F 720 MET cc_start: 0.7828 (mmm) cc_final: 0.7378 (mtp) REVERT: A 230 ILE cc_start: 0.8070 (mp) cc_final: 0.7790 (pt) REVERT: A 233 ARG cc_start: 0.7327 (mtt90) cc_final: 0.6956 (mmm160) REVERT: A 276 MET cc_start: 0.7029 (mmm) cc_final: 0.6238 (mtm) REVERT: A 446 ARG cc_start: 0.8605 (tpp80) cc_final: 0.8217 (tpp-160) REVERT: A 467 MET cc_start: 0.0900 (mtm) cc_final: 0.0028 (mmp) REVERT: A 567 ILE cc_start: 0.8484 (mt) cc_final: 0.8162 (tt) REVERT: A 674 GLU cc_start: 0.8143 (mp0) cc_final: 0.7911 (mp0) outliers start: 99 outliers final: 53 residues processed: 589 average time/residue: 0.3598 time to fit residues: 329.0910 Evaluate side-chains 482 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 429 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain F residue 363 GLN Chi-restraints excluded: chain F residue 427 LYS Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 730 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 235 optimal weight: 0.0970 chunk 192 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 283 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN B 418 GLN ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 GLN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN ** D 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN E 410 HIS ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS A 301 ASN A 319 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25032 Z= 0.324 Angle : 0.786 12.771 33798 Z= 0.412 Chirality : 0.049 0.318 3876 Planarity : 0.006 0.114 4308 Dihedral : 12.557 89.817 3737 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.78 % Favored : 88.13 % Rotamer: Outliers : 4.09 % Allowed : 15.13 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.11 % Twisted Proline : 2.27 % Twisted General : 0.34 % 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: -3.67 (0.14), residues: 3108 helix: -2.22 (0.12), residues: 1347 sheet: -1.89 (0.26), residues: 367 loop : -2.73 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 510 HIS 0.011 0.002 HIS B 417 PHE 0.041 0.002 PHE D 231 TYR 0.019 0.002 TYR C 499 ARG 0.005 0.001 ARG D 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 454 time to evaluate : 2.995 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: B 256 ILE cc_start: 0.8995 (mt) cc_final: 0.8495 (mt) REVERT: B 329 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6396 (mp0) REVERT: B 712 MET cc_start: 0.8713 (tpp) cc_final: 0.8261 (tpp) REVERT: C 238 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7600 (ttm-80) REVERT: C 283 LYS cc_start: 0.8449 (mmmt) cc_final: 0.7659 (mttp) REVERT: C 340 MET cc_start: 0.3642 (ptm) cc_final: 0.3385 (ptm) REVERT: C 435 ASN cc_start: 0.8709 (t0) cc_final: 0.8374 (t0) REVERT: C 442 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7500 (tm-30) REVERT: C 720 MET cc_start: 0.7837 (mmm) cc_final: 0.7315 (mtp) REVERT: D 248 MET cc_start: 0.4159 (mpp) cc_final: 0.3246 (mmm) REVERT: D 273 ILE cc_start: 0.8964 (tp) cc_final: 0.8597 (tt) REVERT: D 276 MET cc_start: 0.6465 (tpt) cc_final: 0.6104 (tpt) REVERT: D 621 LEU cc_start: 0.9020 (tp) cc_final: 0.8705 (tp) REVERT: D 678 GLU cc_start: 0.8010 (tp30) cc_final: 0.7797 (tp30) REVERT: D 712 MET cc_start: 0.8883 (tpp) cc_final: 0.8657 (tpp) REVERT: E 312 GLU cc_start: 0.8110 (mm-30) cc_final: 0.6907 (tm-30) REVERT: E 403 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7832 (mtm110) REVERT: E 440 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7881 (mp0) REVERT: E 561 ASN cc_start: 0.7988 (m110) cc_final: 0.7431 (t0) REVERT: E 712 MET cc_start: 0.7390 (mmm) cc_final: 0.7103 (mtt) REVERT: E 713 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8812 (mt) REVERT: E 727 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7159 (ttm110) REVERT: F 340 MET cc_start: 0.5237 (ptm) cc_final: 0.3670 (mmt) REVERT: F 394 GLU cc_start: 0.6981 (tp30) cc_final: 0.6271 (pm20) REVERT: F 414 MET cc_start: 0.8046 (ttp) cc_final: 0.7735 (ptm) REVERT: F 496 GLN cc_start: 0.4477 (tt0) cc_final: 0.4183 (mp10) REVERT: F 499 TYR cc_start: 0.6095 (p90) cc_final: 0.5810 (p90) REVERT: F 510 TRP cc_start: 0.7707 (p-90) cc_final: 0.7406 (p-90) REVERT: F 655 MET cc_start: 0.8481 (mtm) cc_final: 0.7695 (mtm) REVERT: F 712 MET cc_start: 0.8337 (mmm) cc_final: 0.7998 (tpp) REVERT: F 715 GLU cc_start: 0.7367 (tp30) cc_final: 0.7151 (tp30) REVERT: F 716 MET cc_start: 0.8464 (mtp) cc_final: 0.7560 (mpp) REVERT: F 720 MET cc_start: 0.7733 (mmm) cc_final: 0.7341 (mtp) REVERT: A 233 ARG cc_start: 0.7452 (mtt90) cc_final: 0.6999 (mmm160) REVERT: A 276 MET cc_start: 0.7057 (mmm) cc_final: 0.6227 (mtm) REVERT: A 405 GLN cc_start: 0.5782 (tm-30) cc_final: 0.5268 (tm-30) REVERT: A 467 MET cc_start: 0.0847 (mtm) cc_final: -0.0136 (mmp) REVERT: A 567 ILE cc_start: 0.8721 (mt) cc_final: 0.8259 (tt) REVERT: A 600 VAL cc_start: 0.9065 (t) cc_final: 0.8824 (m) REVERT: A 621 LEU cc_start: 0.8712 (tp) cc_final: 0.8459 (mt) REVERT: A 654 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8165 (tp30) outliers start: 109 outliers final: 69 residues processed: 528 average time/residue: 0.3597 time to fit residues: 298.1236 Evaluate side-chains 473 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 402 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 713 LEU Chi-restraints excluded: chain F residue 363 GLN Chi-restraints excluded: chain F residue 427 LYS Chi-restraints excluded: chain F residue 466 ASP Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 730 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 30.0000 chunk 213 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 301 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 269 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 GLN ** F 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25032 Z= 0.297 Angle : 0.746 13.241 33798 Z= 0.390 Chirality : 0.048 0.304 3876 Planarity : 0.005 0.111 4308 Dihedral : 12.217 89.362 3737 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.78 % Favored : 88.16 % Rotamer: Outliers : 4.35 % Allowed : 16.29 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.11 % Twisted Proline : 3.03 % Twisted General : 0.27 % 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: -3.23 (0.14), residues: 3108 helix: -1.73 (0.13), residues: 1325 sheet: -1.79 (0.27), residues: 362 loop : -2.60 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 510 HIS 0.008 0.001 HIS B 417 PHE 0.027 0.002 PHE D 231 TYR 0.014 0.001 TYR D 502 ARG 0.006 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 421 time to evaluate : 2.762 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: B 220 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8682 (tp) REVERT: B 256 ILE cc_start: 0.9219 (mt) cc_final: 0.8892 (mt) REVERT: B 467 MET cc_start: 0.3067 (mmm) cc_final: 0.2706 (mmm) REVERT: B 712 MET cc_start: 0.8710 (tpp) cc_final: 0.8312 (tpp) REVERT: C 238 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7518 (ttm-80) REVERT: C 247 GLN cc_start: 0.7330 (mt0) cc_final: 0.7092 (mp10) REVERT: C 283 LYS cc_start: 0.8496 (mmmt) cc_final: 0.7664 (mttp) REVERT: C 323 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7579 (m90) REVERT: C 340 MET cc_start: 0.3774 (ptm) cc_final: 0.3504 (ptm) REVERT: C 397 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8346 (pp) REVERT: C 435 ASN cc_start: 0.8608 (t0) cc_final: 0.8270 (t0) REVERT: C 442 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7508 (tm-30) REVERT: C 720 MET cc_start: 0.7780 (mmm) cc_final: 0.7239 (mtp) REVERT: D 248 MET cc_start: 0.4222 (mpp) cc_final: 0.3242 (mmm) REVERT: D 273 ILE cc_start: 0.8961 (tp) cc_final: 0.8601 (tt) REVERT: D 276 MET cc_start: 0.6326 (tpt) cc_final: 0.5965 (tpt) REVERT: D 621 LEU cc_start: 0.8881 (tp) cc_final: 0.8664 (tp) REVERT: D 712 MET cc_start: 0.8889 (tpp) cc_final: 0.8674 (tpp) REVERT: E 226 GLU cc_start: 0.8113 (mp0) cc_final: 0.7648 (mp0) REVERT: E 312 GLU cc_start: 0.8037 (mm-30) cc_final: 0.6870 (tm-30) REVERT: E 403 ARG cc_start: 0.8330 (mtm-85) cc_final: 0.7940 (mtp85) REVERT: E 440 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7946 (mp0) REVERT: E 561 ASN cc_start: 0.8027 (m110) cc_final: 0.7415 (t0) REVERT: E 712 MET cc_start: 0.7491 (mmm) cc_final: 0.7264 (mtt) REVERT: E 713 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8680 (mt) REVERT: E 727 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7056 (ttm110) REVERT: F 340 MET cc_start: 0.5471 (ptm) cc_final: 0.3837 (mmt) REVERT: F 394 GLU cc_start: 0.6978 (tp30) cc_final: 0.6482 (pm20) REVERT: F 414 MET cc_start: 0.7959 (ttp) cc_final: 0.7625 (tmm) REVERT: F 496 GLN cc_start: 0.4657 (tt0) cc_final: 0.4002 (mp10) REVERT: F 499 TYR cc_start: 0.6132 (p90) cc_final: 0.5842 (p90) REVERT: F 510 TRP cc_start: 0.7747 (p-90) cc_final: 0.7412 (p-90) REVERT: F 704 TRP cc_start: 0.8297 (t60) cc_final: 0.8070 (t60) REVERT: F 712 MET cc_start: 0.8314 (mmm) cc_final: 0.7774 (mmm) REVERT: F 715 GLU cc_start: 0.7441 (tp30) cc_final: 0.7211 (tp30) REVERT: F 716 MET cc_start: 0.8577 (mtp) cc_final: 0.7708 (mpp) REVERT: F 720 MET cc_start: 0.7750 (mmm) cc_final: 0.7396 (mtp) REVERT: A 233 ARG cc_start: 0.7422 (mtt90) cc_final: 0.6975 (mmm160) REVERT: A 276 MET cc_start: 0.7050 (mmm) cc_final: 0.6243 (mtm) REVERT: A 297 GLU cc_start: 0.5248 (mp0) cc_final: 0.4740 (mm-30) REVERT: A 453 MET cc_start: 0.5981 (tpt) cc_final: 0.5747 (tpt) REVERT: A 467 MET cc_start: 0.0926 (mtm) cc_final: -0.0081 (mmt) REVERT: A 550 THR cc_start: 0.6783 (m) cc_final: 0.6392 (m) REVERT: A 567 ILE cc_start: 0.8723 (mt) cc_final: 0.8232 (tt) REVERT: A 600 VAL cc_start: 0.9051 (t) cc_final: 0.8822 (m) REVERT: A 621 LEU cc_start: 0.8694 (tp) cc_final: 0.8460 (mt) REVERT: A 654 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8122 (tp30) outliers start: 116 outliers final: 85 residues processed: 496 average time/residue: 0.3387 time to fit residues: 265.9682 Evaluate side-chains 483 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 393 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 565 ILE Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 713 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 363 GLN Chi-restraints excluded: chain F residue 427 LYS Chi-restraints excluded: chain F residue 466 ASP Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 528 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 686 PHE Chi-restraints excluded: chain A residue 730 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 224 optimal weight: 0.0270 chunk 124 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 208 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 270 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 overall best weight: 2.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 ASN ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN ** F 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25032 Z= 0.231 Angle : 0.707 13.111 33798 Z= 0.369 Chirality : 0.046 0.278 3876 Planarity : 0.005 0.108 4308 Dihedral : 11.851 89.184 3737 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.26 % Favored : 88.67 % Rotamer: Outliers : 4.77 % Allowed : 16.82 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.11 % Twisted Proline : 2.27 % Twisted General : 0.23 % 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 (0.15), residues: 3108 helix: -1.28 (0.14), residues: 1308 sheet: -1.61 (0.27), residues: 360 loop : -2.45 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 510 HIS 0.008 0.001 HIS B 417 PHE 0.039 0.002 PHE D 231 TYR 0.018 0.001 TYR F 259 ARG 0.008 0.000 ARG D 516 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 420 time to evaluate : 2.800 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: B 220 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8762 (tp) REVERT: B 240 PHE cc_start: 0.5628 (m-80) cc_final: 0.5178 (m-80) REVERT: B 256 ILE cc_start: 0.9206 (mt) cc_final: 0.8858 (mt) REVERT: B 458 LYS cc_start: 0.0726 (OUTLIER) cc_final: 0.0176 (ptpp) REVERT: B 519 ASP cc_start: 0.7588 (p0) cc_final: 0.6288 (t0) REVERT: B 606 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6680 (pm20) REVERT: B 712 MET cc_start: 0.8673 (tpp) cc_final: 0.8280 (tpp) REVERT: B 715 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7502 (mm-30) REVERT: C 238 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7513 (ttm-80) REVERT: C 247 GLN cc_start: 0.7175 (mt0) cc_final: 0.6925 (mp10) REVERT: C 283 LYS cc_start: 0.8465 (mmmt) cc_final: 0.7608 (mttp) REVERT: C 323 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7564 (m90) REVERT: C 435 ASN cc_start: 0.8590 (t0) cc_final: 0.8308 (t0) REVERT: C 442 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 449 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6902 (pt0) REVERT: C 720 MET cc_start: 0.7761 (mmm) cc_final: 0.7225 (mtp) REVERT: D 248 MET cc_start: 0.4188 (mpp) cc_final: 0.3210 (mmm) REVERT: D 273 ILE cc_start: 0.8917 (tp) cc_final: 0.8528 (tt) REVERT: D 276 MET cc_start: 0.6647 (tpt) cc_final: 0.6151 (tpt) REVERT: D 516 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.7255 (ttp80) REVERT: D 565 ILE cc_start: 0.8997 (mt) cc_final: 0.8720 (tp) REVERT: D 712 MET cc_start: 0.8855 (tpp) cc_final: 0.8637 (tpp) REVERT: E 312 GLU cc_start: 0.7956 (mm-30) cc_final: 0.6548 (tm-30) REVERT: E 401 LYS cc_start: 0.8068 (tptt) cc_final: 0.7774 (tptt) REVERT: E 403 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.7782 (mtp85) REVERT: E 440 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7946 (mp0) REVERT: E 498 ASP cc_start: 0.6513 (m-30) cc_final: 0.6084 (m-30) REVERT: E 561 ASN cc_start: 0.8004 (m110) cc_final: 0.7387 (t0) REVERT: E 712 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7259 (mtt) REVERT: E 727 ARG cc_start: 0.7597 (mtm-85) cc_final: 0.6976 (ttm110) REVERT: F 340 MET cc_start: 0.5601 (ptm) cc_final: 0.3922 (mmt) REVERT: F 496 GLN cc_start: 0.4939 (tt0) cc_final: 0.4199 (mp10) REVERT: F 499 TYR cc_start: 0.6029 (p90) cc_final: 0.5789 (p90) REVERT: F 510 TRP cc_start: 0.7711 (p-90) cc_final: 0.7361 (p-90) REVERT: F 650 ASP cc_start: 0.8002 (p0) cc_final: 0.7724 (t0) REVERT: F 704 TRP cc_start: 0.8266 (t60) cc_final: 0.8058 (t60) REVERT: F 712 MET cc_start: 0.8264 (mmm) cc_final: 0.7980 (tpp) REVERT: F 716 MET cc_start: 0.8570 (mtp) cc_final: 0.7714 (mpp) REVERT: F 720 MET cc_start: 0.7782 (mmm) cc_final: 0.7386 (mtp) REVERT: A 229 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6658 (t0) REVERT: A 230 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7609 (pt) REVERT: A 233 ARG cc_start: 0.7361 (mtt90) cc_final: 0.7008 (mmm160) REVERT: A 276 MET cc_start: 0.7001 (mmm) cc_final: 0.6207 (mtm) REVERT: A 297 GLU cc_start: 0.5361 (mp0) cc_final: 0.4782 (mm-30) REVERT: A 405 GLN cc_start: 0.6029 (tm-30) cc_final: 0.5558 (tm-30) REVERT: A 415 ARG cc_start: 0.7310 (mtt90) cc_final: 0.7064 (mtt90) REVERT: A 440 GLU cc_start: 0.5413 (tm-30) cc_final: 0.5132 (tm-30) REVERT: A 467 MET cc_start: 0.0957 (mtm) cc_final: -0.0108 (mmt) REVERT: A 567 ILE cc_start: 0.8688 (mt) cc_final: 0.8181 (tt) REVERT: A 600 VAL cc_start: 0.9030 (t) cc_final: 0.8788 (m) REVERT: A 621 LEU cc_start: 0.8589 (tp) cc_final: 0.8372 (mt) outliers start: 127 outliers final: 83 residues processed: 505 average time/residue: 0.3427 time to fit residues: 276.3094 Evaluate side-chains 485 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 393 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 527 GLN Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 565 ILE Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 712 MET Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 363 GLN Chi-restraints excluded: chain F residue 427 LYS Chi-restraints excluded: chain F residue 466 ASP Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 4.9990 chunk 271 optimal weight: 0.0870 chunk 59 optimal weight: 4.9990 chunk 177 optimal weight: 0.0870 chunk 74 optimal weight: 4.9990 chunk 301 optimal weight: 0.5980 chunk 250 optimal weight: 10.0000 chunk 139 optimal weight: 0.0980 chunk 25 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 158 optimal weight: 0.0970 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN C 435 ASN C 449 GLN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN E 353 GLN E 435 ASN F 449 GLN ** F 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25032 Z= 0.156 Angle : 0.674 12.395 33798 Z= 0.350 Chirality : 0.045 0.267 3876 Planarity : 0.005 0.092 4308 Dihedral : 11.257 85.906 3737 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.01 % Favored : 89.93 % Rotamer: Outliers : 3.72 % Allowed : 18.54 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.14 % Twisted Proline : 1.52 % Twisted General : 0.20 % 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: -2.41 (0.15), residues: 3108 helix: -0.89 (0.14), residues: 1320 sheet: -1.37 (0.28), residues: 359 loop : -2.33 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 510 HIS 0.010 0.001 HIS B 417 PHE 0.022 0.001 PHE D 231 TYR 0.012 0.001 TYR F 259 ARG 0.006 0.000 ARG D 516 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 482 time to evaluate : 2.921 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: B 220 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8626 (tp) REVERT: B 240 PHE cc_start: 0.5438 (m-80) cc_final: 0.5039 (m-80) REVERT: B 256 ILE cc_start: 0.9132 (mt) cc_final: 0.8809 (mt) REVERT: B 329 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6449 (mp0) REVERT: B 453 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8355 (mtt) REVERT: B 519 ASP cc_start: 0.7305 (p0) cc_final: 0.6428 (t0) REVERT: B 612 VAL cc_start: 0.9512 (OUTLIER) cc_final: 0.9269 (m) REVERT: B 712 MET cc_start: 0.8574 (tpp) cc_final: 0.8153 (tpp) REVERT: C 247 GLN cc_start: 0.6974 (mt0) cc_final: 0.6754 (mp10) REVERT: C 283 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7289 (mttp) REVERT: C 397 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8261 (pp) REVERT: C 435 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8031 (t0) REVERT: C 449 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6884 (pt0) REVERT: C 720 MET cc_start: 0.7710 (mmm) cc_final: 0.7175 (mtp) REVERT: D 224 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7103 (t0) REVERT: D 232 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8149 (ttm170) REVERT: D 248 MET cc_start: 0.3897 (mpp) cc_final: 0.3033 (mmm) REVERT: D 712 MET cc_start: 0.8813 (tpp) cc_final: 0.8543 (tpp) REVERT: E 335 LYS cc_start: 0.7621 (mtpt) cc_final: 0.7205 (mtpp) REVERT: E 498 ASP cc_start: 0.6498 (m-30) cc_final: 0.6157 (m-30) REVERT: E 561 ASN cc_start: 0.7919 (m110) cc_final: 0.7348 (t0) REVERT: E 727 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.6903 (ttm110) REVERT: F 340 MET cc_start: 0.5650 (ptm) cc_final: 0.4014 (mmt) REVERT: F 394 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6321 (pm20) REVERT: F 510 TRP cc_start: 0.7658 (p-90) cc_final: 0.7378 (p-90) REVERT: F 650 ASP cc_start: 0.8022 (p0) cc_final: 0.7816 (t0) REVERT: F 720 MET cc_start: 0.7888 (mmm) cc_final: 0.7456 (mtp) REVERT: A 230 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7556 (pt) REVERT: A 233 ARG cc_start: 0.7247 (mtt90) cc_final: 0.6954 (mmm160) REVERT: A 276 MET cc_start: 0.6795 (mmm) cc_final: 0.5980 (mtm) REVERT: A 405 GLN cc_start: 0.5973 (tm-30) cc_final: 0.5548 (tm-30) REVERT: A 415 ARG cc_start: 0.7413 (mtt90) cc_final: 0.7175 (mtt90) REVERT: A 440 GLU cc_start: 0.5577 (tm-30) cc_final: 0.5300 (tm-30) REVERT: A 467 MET cc_start: 0.0683 (mtm) cc_final: -0.0252 (mmt) REVERT: A 542 GLU cc_start: 0.7776 (tt0) cc_final: 0.7502 (tt0) REVERT: A 550 THR cc_start: 0.7257 (m) cc_final: 0.6957 (m) REVERT: A 567 ILE cc_start: 0.8705 (mt) cc_final: 0.8230 (tt) REVERT: A 680 LEU cc_start: 0.8276 (mp) cc_final: 0.7110 (tp) outliers start: 99 outliers final: 50 residues processed: 549 average time/residue: 0.3362 time to fit residues: 295.7099 Evaluate side-chains 459 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 400 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 435 ASN Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain D residue 527 GLN Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 520 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 588 ILE Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 363 GLN Chi-restraints excluded: chain F residue 466 ASP Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 170 optimal weight: 0.5980 chunk 254 optimal weight: 5.9990 chunk 168 optimal weight: 30.0000 chunk 300 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 ASN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN D 496 GLN E 666 HIS ** E 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25032 Z= 0.307 Angle : 0.740 13.603 33798 Z= 0.380 Chirality : 0.048 0.325 3876 Planarity : 0.005 0.098 4308 Dihedral : 11.359 88.518 3737 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.39 % Favored : 88.55 % Rotamer: Outliers : 4.20 % Allowed : 19.48 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.11 % Twisted Proline : 2.27 % Twisted General : 0.23 % 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: -2.40 (0.15), residues: 3108 helix: -0.84 (0.14), residues: 1339 sheet: -1.42 (0.27), residues: 371 loop : -2.38 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 510 HIS 0.007 0.001 HIS C 410 PHE 0.027 0.002 PHE D 231 TYR 0.028 0.002 TYR B 611 ARG 0.009 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 388 time to evaluate : 3.010 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: B 240 PHE cc_start: 0.5822 (m-80) cc_final: 0.5399 (m-80) REVERT: B 256 ILE cc_start: 0.9203 (mt) cc_final: 0.8899 (mt) REVERT: B 453 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8314 (mtp) REVERT: B 519 ASP cc_start: 0.7465 (p0) cc_final: 0.6607 (t0) REVERT: B 606 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6721 (pm20) REVERT: B 612 VAL cc_start: 0.9551 (OUTLIER) cc_final: 0.9216 (m) REVERT: B 712 MET cc_start: 0.8621 (tpp) cc_final: 0.8218 (tpp) REVERT: B 715 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7332 (mm-30) REVERT: C 239 VAL cc_start: 0.7021 (OUTLIER) cc_final: 0.6759 (p) REVERT: C 247 GLN cc_start: 0.7173 (mt0) cc_final: 0.6897 (mp10) REVERT: C 283 LYS cc_start: 0.8533 (mmmt) cc_final: 0.7661 (mttp) REVERT: C 397 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8350 (pp) REVERT: C 720 MET cc_start: 0.7738 (mmm) cc_final: 0.7226 (mtp) REVERT: D 232 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8230 (ttm170) REVERT: D 248 MET cc_start: 0.4334 (mpp) cc_final: 0.3389 (mmm) REVERT: D 276 MET cc_start: 0.6081 (tpt) cc_final: 0.5631 (tpt) REVERT: D 712 MET cc_start: 0.8893 (tpp) cc_final: 0.8600 (tpp) REVERT: E 312 GLU cc_start: 0.8133 (mm-30) cc_final: 0.6683 (tm-30) REVERT: E 313 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6435 (mt0) REVERT: E 498 ASP cc_start: 0.6556 (m-30) cc_final: 0.6223 (m-30) REVERT: E 561 ASN cc_start: 0.8027 (m110) cc_final: 0.7487 (t0) REVERT: E 727 ARG cc_start: 0.7625 (mtm-85) cc_final: 0.6932 (ttm110) REVERT: F 340 MET cc_start: 0.5619 (ptm) cc_final: 0.3773 (mmt) REVERT: F 394 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6461 (pm20) REVERT: F 510 TRP cc_start: 0.7765 (p-90) cc_final: 0.7450 (p-90) REVERT: F 650 ASP cc_start: 0.8094 (p0) cc_final: 0.7893 (t0) REVERT: F 720 MET cc_start: 0.7752 (mmm) cc_final: 0.7349 (mtp) REVERT: A 233 ARG cc_start: 0.7384 (mtt90) cc_final: 0.7044 (mmm160) REVERT: A 276 MET cc_start: 0.6846 (mmm) cc_final: 0.6016 (mtm) REVERT: A 405 GLN cc_start: 0.6083 (tm-30) cc_final: 0.5600 (tm-30) REVERT: A 413 ARG cc_start: 0.6483 (ttp-110) cc_final: 0.5919 (ptt180) REVERT: A 415 ARG cc_start: 0.7404 (mtt90) cc_final: 0.7176 (mtt90) REVERT: A 440 GLU cc_start: 0.5546 (tm-30) cc_final: 0.5235 (tm-30) REVERT: A 442 GLU cc_start: 0.7681 (pp20) cc_final: 0.7430 (pp20) REVERT: A 467 MET cc_start: 0.0939 (mtm) cc_final: -0.0081 (mmt) REVERT: A 567 ILE cc_start: 0.8759 (mt) cc_final: 0.8240 (tt) REVERT: A 620 ASN cc_start: 0.8672 (t0) cc_final: 0.8391 (t0) REVERT: A 716 MET cc_start: 0.7769 (ttt) cc_final: 0.7471 (ttm) outliers start: 112 outliers final: 73 residues processed: 470 average time/residue: 0.3557 time to fit residues: 267.3215 Evaluate side-chains 455 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 375 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain D residue 527 GLN Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 565 ILE Chi-restraints excluded: chain E residue 569 SER Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 466 ASP Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.0060 chunk 191 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 236 optimal weight: 20.0000 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25032 Z= 0.221 Angle : 0.705 13.268 33798 Z= 0.363 Chirality : 0.047 0.288 3876 Planarity : 0.005 0.099 4308 Dihedral : 11.218 88.840 3737 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.42 % Favored : 89.51 % Rotamer: Outliers : 3.75 % Allowed : 20.08 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.14 % Twisted Proline : 0.76 % Twisted General : 0.20 % 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: -2.22 (0.15), residues: 3108 helix: -0.65 (0.15), residues: 1327 sheet: -1.27 (0.27), residues: 369 loop : -2.32 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 510 HIS 0.008 0.001 HIS B 417 PHE 0.041 0.002 PHE D 231 TYR 0.026 0.001 TYR B 611 ARG 0.009 0.000 ARG D 516 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 396 time to evaluate : 3.204 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: B 226 GLU cc_start: 0.8799 (pp20) cc_final: 0.8552 (pp20) REVERT: B 240 PHE cc_start: 0.5651 (m-80) cc_final: 0.5284 (m-80) REVERT: B 256 ILE cc_start: 0.9235 (mt) cc_final: 0.8920 (mt) REVERT: B 453 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8268 (mtp) REVERT: B 519 ASP cc_start: 0.7213 (p0) cc_final: 0.6421 (t0) REVERT: B 612 VAL cc_start: 0.9555 (OUTLIER) cc_final: 0.9226 (m) REVERT: B 712 MET cc_start: 0.8591 (tpp) cc_final: 0.8229 (tpp) REVERT: C 247 GLN cc_start: 0.7155 (mt0) cc_final: 0.6874 (mp10) REVERT: C 283 LYS cc_start: 0.8428 (mmmt) cc_final: 0.7537 (mttp) REVERT: C 297 GLU cc_start: 0.4327 (mp0) cc_final: 0.3470 (pm20) REVERT: C 397 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8366 (pp) REVERT: C 435 ASN cc_start: 0.8522 (t0) cc_final: 0.8185 (t0) REVERT: C 720 MET cc_start: 0.7725 (mmm) cc_final: 0.7311 (mtp) REVERT: D 232 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8158 (ttm170) REVERT: D 248 MET cc_start: 0.4237 (mpp) cc_final: 0.3315 (mmm) REVERT: D 276 MET cc_start: 0.6077 (tpt) cc_final: 0.5597 (tpt) REVERT: D 453 MET cc_start: 0.8624 (ttp) cc_final: 0.7828 (tpt) REVERT: D 481 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8454 (mm) REVERT: D 712 MET cc_start: 0.8873 (tpp) cc_final: 0.8605 (tpp) REVERT: E 312 GLU cc_start: 0.8124 (mm-30) cc_final: 0.6673 (tm-30) REVERT: E 313 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.6257 (mt0) REVERT: E 337 ARG cc_start: 0.5029 (OUTLIER) cc_final: 0.3627 (pmt100) REVERT: E 498 ASP cc_start: 0.6593 (m-30) cc_final: 0.6330 (m-30) REVERT: E 561 ASN cc_start: 0.8019 (m110) cc_final: 0.7456 (t0) REVERT: E 727 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7051 (ttm110) REVERT: F 340 MET cc_start: 0.5709 (ptm) cc_final: 0.3928 (mmt) REVERT: F 510 TRP cc_start: 0.7672 (p-90) cc_final: 0.7351 (p-90) REVERT: F 666 HIS cc_start: 0.7415 (t70) cc_final: 0.7007 (t-90) REVERT: F 720 MET cc_start: 0.7782 (mmm) cc_final: 0.7441 (mtp) REVERT: A 230 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7690 (pt) REVERT: A 233 ARG cc_start: 0.7314 (mtt90) cc_final: 0.7023 (mmm160) REVERT: A 276 MET cc_start: 0.6756 (mmm) cc_final: 0.5898 (mtm) REVERT: A 297 GLU cc_start: 0.5782 (mp0) cc_final: 0.5213 (mm-30) REVERT: A 405 GLN cc_start: 0.6046 (tm-30) cc_final: 0.5578 (tm-30) REVERT: A 413 ARG cc_start: 0.6371 (ttp-110) cc_final: 0.5837 (ptt180) REVERT: A 440 GLU cc_start: 0.5510 (tm-30) cc_final: 0.5205 (tm-30) REVERT: A 442 GLU cc_start: 0.7782 (pp20) cc_final: 0.7556 (pp20) REVERT: A 467 MET cc_start: 0.1064 (mtm) cc_final: 0.0012 (mmt) REVERT: A 567 ILE cc_start: 0.8779 (mt) cc_final: 0.8284 (tt) REVERT: A 620 ASN cc_start: 0.8588 (t0) cc_final: 0.8306 (t0) REVERT: A 680 LEU cc_start: 0.8226 (mp) cc_final: 0.7093 (tp) outliers start: 100 outliers final: 70 residues processed: 468 average time/residue: 0.3725 time to fit residues: 278.3607 Evaluate side-chains 456 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 378 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 527 GLN Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 569 SER Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 366 ASN Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 chunk 262 optimal weight: 40.0000 chunk 280 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 chunk 265 optimal weight: 8.9990 chunk 279 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN D 530 ASN E 697 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25032 Z= 0.322 Angle : 0.756 15.103 33798 Z= 0.388 Chirality : 0.049 0.230 3876 Planarity : 0.005 0.102 4308 Dihedral : 11.384 89.411 3737 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.10 % Favored : 87.84 % Rotamer: Outliers : 3.79 % Allowed : 20.53 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.14 % Twisted Proline : 2.27 % Twisted General : 0.20 % 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: -2.31 (0.15), residues: 3108 helix: -0.74 (0.14), residues: 1347 sheet: -1.35 (0.27), residues: 371 loop : -2.37 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 510 HIS 0.007 0.001 HIS B 417 PHE 0.039 0.002 PHE D 231 TYR 0.013 0.002 TYR C 259 ARG 0.014 0.001 ARG D 516 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 390 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6576 (ttm170) REVERT: B 240 PHE cc_start: 0.5879 (m-80) cc_final: 0.5378 (m-80) REVERT: B 256 ILE cc_start: 0.9266 (mt) cc_final: 0.8880 (mt) REVERT: B 453 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8291 (mtp) REVERT: B 519 ASP cc_start: 0.7200 (p0) cc_final: 0.6328 (t0) REVERT: B 606 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: B 712 MET cc_start: 0.8654 (tpp) cc_final: 0.8282 (tpp) REVERT: C 238 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7647 (ttm-80) REVERT: C 247 GLN cc_start: 0.7395 (mt0) cc_final: 0.7067 (mp10) REVERT: C 283 LYS cc_start: 0.8535 (mmmt) cc_final: 0.7722 (mttp) REVERT: C 397 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8400 (pp) REVERT: C 696 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7638 (mp10) REVERT: C 720 MET cc_start: 0.7718 (mmm) cc_final: 0.7437 (mtp) REVERT: D 220 ILE cc_start: 0.8551 (mt) cc_final: 0.8276 (tt) REVERT: D 232 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8157 (ttm170) REVERT: D 248 MET cc_start: 0.4045 (mpp) cc_final: 0.3190 (mmm) REVERT: D 453 MET cc_start: 0.8625 (ttp) cc_final: 0.7952 (tpt) REVERT: D 481 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8492 (mm) REVERT: D 712 MET cc_start: 0.8874 (tpp) cc_final: 0.8610 (tpp) REVERT: E 312 GLU cc_start: 0.8231 (mm-30) cc_final: 0.6644 (tm-30) REVERT: E 313 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6382 (mt0) REVERT: E 337 ARG cc_start: 0.5151 (OUTLIER) cc_final: 0.3908 (pmt100) REVERT: E 498 ASP cc_start: 0.6577 (m-30) cc_final: 0.6319 (m-30) REVERT: E 561 ASN cc_start: 0.8052 (m110) cc_final: 0.7510 (t0) REVERT: E 727 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7027 (ttm110) REVERT: F 233 ARG cc_start: 0.4932 (mtt90) cc_final: 0.4608 (mpt180) REVERT: F 340 MET cc_start: 0.5747 (ptm) cc_final: 0.3951 (mmt) REVERT: F 510 TRP cc_start: 0.7852 (p-90) cc_final: 0.7369 (p-90) REVERT: F 655 MET cc_start: 0.8470 (mtm) cc_final: 0.8040 (mtm) REVERT: F 666 HIS cc_start: 0.7382 (t70) cc_final: 0.7014 (t-90) REVERT: F 716 MET cc_start: 0.8544 (mtp) cc_final: 0.7651 (mpp) REVERT: F 720 MET cc_start: 0.7788 (mmm) cc_final: 0.7385 (mtp) REVERT: A 230 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7618 (pt) REVERT: A 233 ARG cc_start: 0.7419 (mtt90) cc_final: 0.7181 (mmm160) REVERT: A 276 MET cc_start: 0.6672 (mmm) cc_final: 0.5844 (mtm) REVERT: A 297 GLU cc_start: 0.6029 (mp0) cc_final: 0.5469 (mm-30) REVERT: A 440 GLU cc_start: 0.5500 (tm-30) cc_final: 0.5135 (tm-30) REVERT: A 442 GLU cc_start: 0.7781 (pp20) cc_final: 0.7544 (pp20) REVERT: A 467 MET cc_start: 0.1122 (mtm) cc_final: 0.0050 (mmt) REVERT: A 620 ASN cc_start: 0.8694 (t0) cc_final: 0.8381 (t0) REVERT: A 680 LEU cc_start: 0.8274 (mp) cc_final: 0.7056 (tp) REVERT: A 716 MET cc_start: 0.7866 (ttt) cc_final: 0.7627 (ttm) outliers start: 101 outliers final: 74 residues processed: 463 average time/residue: 0.3449 time to fit residues: 252.6179 Evaluate side-chains 456 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 371 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 696 GLN Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 527 GLN Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 569 SER Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 366 ASN Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 286 optimal weight: 0.0970 chunk 247 optimal weight: 4.9990 chunk 25 optimal weight: 0.0060 chunk 191 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN C 435 ASN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25032 Z= 0.178 Angle : 0.711 20.694 33798 Z= 0.362 Chirality : 0.046 0.248 3876 Planarity : 0.005 0.090 4308 Dihedral : 11.024 87.517 3737 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.68 % Favored : 90.25 % Rotamer: Outliers : 3.15 % Allowed : 21.55 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.14 % Twisted Proline : 1.52 % Twisted General : 0.20 % 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: -1.98 (0.15), residues: 3108 helix: -0.39 (0.15), residues: 1328 sheet: -1.15 (0.28), residues: 357 loop : -2.27 (0.17), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 510 HIS 0.005 0.001 HIS F 456 PHE 0.024 0.001 PHE D 235 TYR 0.018 0.001 TYR C 499 ARG 0.007 0.000 ARG E 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 394 time to evaluate : 2.871 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: B 240 PHE cc_start: 0.5654 (m-80) cc_final: 0.5310 (m-80) REVERT: B 256 ILE cc_start: 0.9294 (mt) cc_final: 0.8960 (mt) REVERT: B 409 ILE cc_start: 0.8544 (mt) cc_final: 0.8267 (tp) REVERT: B 453 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8380 (mtp) REVERT: B 519 ASP cc_start: 0.7037 (p0) cc_final: 0.6260 (t0) REVERT: B 712 MET cc_start: 0.8627 (tpp) cc_final: 0.8267 (tpp) REVERT: B 715 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7352 (mm-30) REVERT: C 238 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7558 (ttm-80) REVERT: C 283 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7431 (mttp) REVERT: C 397 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8341 (pp) REVERT: C 414 MET cc_start: 0.6560 (ttt) cc_final: 0.6223 (ttm) REVERT: C 435 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8133 (t0) REVERT: C 442 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7022 (tm-30) REVERT: C 720 MET cc_start: 0.7654 (mmm) cc_final: 0.7402 (mtp) REVERT: D 220 ILE cc_start: 0.8401 (mt) cc_final: 0.8125 (tt) REVERT: D 232 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8124 (ttm170) REVERT: D 248 MET cc_start: 0.4484 (mpp) cc_final: 0.3594 (mmm) REVERT: D 276 MET cc_start: 0.5899 (tpt) cc_final: 0.5390 (tpt) REVERT: D 340 MET cc_start: 0.3893 (mmt) cc_final: 0.1009 (ppp) REVERT: D 453 MET cc_start: 0.8596 (ttp) cc_final: 0.7832 (tpt) REVERT: D 481 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8455 (mm) REVERT: D 712 MET cc_start: 0.8866 (tpp) cc_final: 0.8555 (tpp) REVERT: E 229 ASP cc_start: 0.8920 (t0) cc_final: 0.8437 (m-30) REVERT: E 312 GLU cc_start: 0.8118 (mm-30) cc_final: 0.6620 (tm-30) REVERT: E 313 GLN cc_start: 0.6440 (OUTLIER) cc_final: 0.6016 (mt0) REVERT: E 467 MET cc_start: 0.4305 (mmp) cc_final: 0.4031 (mmp) REVERT: E 561 ASN cc_start: 0.7999 (m110) cc_final: 0.7433 (t0) REVERT: E 657 MET cc_start: 0.8374 (ttp) cc_final: 0.8144 (ttp) REVERT: E 727 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7013 (ttm110) REVERT: F 233 ARG cc_start: 0.4852 (mtt90) cc_final: 0.4420 (mpt180) REVERT: F 340 MET cc_start: 0.5718 (ptm) cc_final: 0.3948 (mmt) REVERT: F 366 ASN cc_start: 0.5788 (OUTLIER) cc_final: 0.5513 (p0) REVERT: F 510 TRP cc_start: 0.7768 (p-90) cc_final: 0.7295 (p-90) REVERT: F 621 LEU cc_start: 0.8989 (tp) cc_final: 0.8655 (tt) REVERT: F 666 HIS cc_start: 0.7287 (t70) cc_final: 0.6928 (t-90) REVERT: F 716 MET cc_start: 0.8517 (mtp) cc_final: 0.7601 (mpp) REVERT: F 720 MET cc_start: 0.7790 (mmm) cc_final: 0.7361 (mtp) REVERT: A 230 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7589 (pt) REVERT: A 276 MET cc_start: 0.6569 (mmm) cc_final: 0.5762 (mtm) REVERT: A 297 GLU cc_start: 0.5924 (mp0) cc_final: 0.5254 (mm-30) REVERT: A 347 HIS cc_start: 0.6008 (OUTLIER) cc_final: 0.5794 (m90) REVERT: A 405 GLN cc_start: 0.5986 (tm-30) cc_final: 0.5498 (tm-30) REVERT: A 440 GLU cc_start: 0.5557 (tm-30) cc_final: 0.5229 (tm-30) REVERT: A 442 GLU cc_start: 0.7754 (pp20) cc_final: 0.7531 (pp20) REVERT: A 467 MET cc_start: 0.1095 (mtm) cc_final: 0.0094 (mmt) REVERT: A 542 GLU cc_start: 0.7721 (tt0) cc_final: 0.7495 (tt0) REVERT: A 680 LEU cc_start: 0.8255 (mp) cc_final: 0.7130 (tp) REVERT: A 716 MET cc_start: 0.7708 (ttt) cc_final: 0.7492 (ttm) outliers start: 84 outliers final: 60 residues processed: 454 average time/residue: 0.3394 time to fit residues: 245.9021 Evaluate side-chains 440 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 370 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 435 ASN Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 527 GLN Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 366 ASN Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 247 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 254 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** 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 = 0.4066 r_free = 0.4066 target = 0.167122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131863 restraints weight = 43062.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.135072 restraints weight = 24503.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137124 restraints weight = 17045.846| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25032 Z= 0.180 Angle : 0.703 15.245 33798 Z= 0.359 Chirality : 0.046 0.247 3876 Planarity : 0.005 0.076 4308 Dihedral : 10.763 86.360 3737 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.36 % Favored : 89.58 % Rotamer: Outliers : 2.74 % Allowed : 22.03 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.14 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.85 (0.15), residues: 3108 helix: -0.27 (0.15), residues: 1320 sheet: -1.02 (0.28), residues: 348 loop : -2.22 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 510 HIS 0.013 0.001 HIS A 456 PHE 0.027 0.002 PHE B 235 TYR 0.019 0.001 TYR C 499 ARG 0.007 0.000 ARG E 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5772.98 seconds wall clock time: 104 minutes 33.08 seconds (6273.08 seconds total)