Starting phenix.real_space_refine on Sun Feb 18 18:16:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v11_21009/02_2024/6v11_21009_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v11_21009/02_2024/6v11_21009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v11_21009/02_2024/6v11_21009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v11_21009/02_2024/6v11_21009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v11_21009/02_2024/6v11_21009_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v11_21009/02_2024/6v11_21009_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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 10 5.49 5 S 123 5.16 5 C 14250 2.51 5 N 3968 2.21 5 O 4275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C ARG 588": "NH1" <-> "NH2" Residue "C GLU 636": "OE1" <-> "OE2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 588": "NH1" <-> "NH2" Residue "F ARG 594": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22626 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3798 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain breaks: 3 Chain: "B" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3829 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 472} Chain breaks: 3 Chain: "C" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3883 Classifications: {'peptide': 503} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 478} Chain breaks: 4 Chain: "D" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3594 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 441} Chain breaks: 5 Chain: "E" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3558 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 441} Chain breaks: 5 Chain: "F" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3829 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 24, 'TRANS': 471} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.82, per 1000 atoms: 0.52 Number of scatterers: 22626 At special positions: 0 Unit cell: (133.4, 120.75, 155.25, 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 123 16.00 P 10 15.00 O 4275 8.00 N 3968 7.00 C 14250 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: 8.28 Conformation dependent library (CDL) restraints added in 3.9 seconds 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5404 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 24 sheets defined 39.0% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.765A pdb=" N MET A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 320 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 365 through 373 removed outlier: 3.736A pdb=" N LYS A 371 " --> pdb=" O GLN A 367 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.560A pdb=" N LEU A 441 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 525 through 533 Processing helix chain 'A' and resid 542 through 561 Processing helix chain 'A' and resid 575 through 578 No H-bonds generated for 'chain 'A' and resid 575 through 578' Processing helix chain 'A' and resid 633 through 648 removed outlier: 3.892A pdb=" N ARG A 648 " --> pdb=" O VAL A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 661 No H-bonds generated for 'chain 'A' and resid 658 through 661' Processing helix chain 'A' and resid 681 through 693 Processing helix chain 'A' and resid 719 through 728 removed outlier: 3.591A pdb=" N ALA A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 746 removed outlier: 5.211A pdb=" N ARG A 742 " --> pdb=" O ASP A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 763 through 768 removed outlier: 3.905A pdb=" N ALA A 768 " --> pdb=" O ASP A 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 265 through 280 removed outlier: 3.813A pdb=" N LYS B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 300 removed outlier: 3.657A pdb=" N MET B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 320 Processing helix chain 'B' and resid 328 through 343 removed outlier: 3.718A pdb=" N ASP B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 373 removed outlier: 3.760A pdb=" N ALA B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 413 Processing helix chain 'B' and resid 439 through 442 removed outlier: 3.697A pdb=" N GLU B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 446 through 449 No H-bonds generated for 'chain 'B' and resid 446 through 449' Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 481 through 484 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 542 through 560 Processing helix chain 'B' and resid 632 through 648 Processing helix chain 'B' and resid 650 through 652 No H-bonds generated for 'chain 'B' and resid 650 through 652' Processing helix chain 'B' and resid 658 through 661 No H-bonds generated for 'chain 'B' and resid 658 through 661' Processing helix chain 'B' and resid 682 through 693 Processing helix chain 'B' and resid 719 through 728 Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 743 through 745 No H-bonds generated for 'chain 'B' and resid 743 through 745' Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 763 through 767 Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 265 through 280 removed outlier: 4.083A pdb=" N MET C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 329 through 343 Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 405 through 413 Processing helix chain 'C' and resid 437 through 440 No H-bonds generated for 'chain 'C' and resid 437 through 440' Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.849A pdb=" N ASP C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ARG C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 479 through 484' Processing helix chain 'C' and resid 495 through 505 Processing helix chain 'C' and resid 525 through 531 Processing helix chain 'C' and resid 542 through 560 Processing helix chain 'C' and resid 575 through 578 No H-bonds generated for 'chain 'C' and resid 575 through 578' Processing helix chain 'C' and resid 631 through 648 removed outlier: 3.901A pdb=" N GLN C 635 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 637 " --> pdb=" O VAL C 633 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 661 No H-bonds generated for 'chain 'C' and resid 658 through 661' Processing helix chain 'C' and resid 682 through 693 Processing helix chain 'C' and resid 719 through 728 Processing helix chain 'C' and resid 738 through 744 removed outlier: 4.913A pdb=" N ARG C 742 " --> pdb=" O ASP C 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 259 removed outlier: 3.522A pdb=" N ILE D 258 " --> pdb=" O LYS D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 280 removed outlier: 3.745A pdb=" N MET D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 300 removed outlier: 4.519A pdb=" N MET D 298 " --> pdb=" O TYR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 322 removed outlier: 3.904A pdb=" N ASP D 321 " --> pdb=" O GLN D 317 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N THR D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 343 Processing helix chain 'D' and resid 362 through 373 removed outlier: 4.283A pdb=" N GLY D 366 " --> pdb=" O LYS D 362 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLN D 367 " --> pdb=" O THR D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 441 through 444 No H-bonds generated for 'chain 'D' and resid 441 through 444' Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'D' and resid 479 through 484 removed outlier: 4.119A pdb=" N ARG D 484 " --> pdb=" O PRO D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 507 through 511 Processing helix chain 'D' and resid 525 through 533 Processing helix chain 'D' and resid 542 through 557 Processing helix chain 'D' and resid 633 through 648 Processing helix chain 'D' and resid 656 through 661 removed outlier: 4.087A pdb=" N TYR D 659 " --> pdb=" O PRO D 656 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS D 661 " --> pdb=" O PHE D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 693 Processing helix chain 'D' and resid 719 through 728 removed outlier: 3.698A pdb=" N ALA D 725 " --> pdb=" O GLU D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 744 removed outlier: 3.589A pdb=" N LYS D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG D 742 " --> pdb=" O ASP D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 754 Processing helix chain 'D' and resid 764 through 767 No H-bonds generated for 'chain 'D' and resid 764 through 767' Processing helix chain 'E' and resid 255 through 260 Processing helix chain 'E' and resid 265 through 278 removed outlier: 4.213A pdb=" N GLU E 269 " --> pdb=" O LYS E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 removed outlier: 3.581A pdb=" N THR E 289 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL E 291 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG E 292 " --> pdb=" O THR E 289 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR E 294 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP E 296 " --> pdb=" O GLY E 293 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TRP E 297 " --> pdb=" O TYR E 294 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET E 298 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 343 Processing helix chain 'E' and resid 365 through 373 Processing helix chain 'E' and resid 405 through 413 Processing helix chain 'E' and resid 441 through 444 No H-bonds generated for 'chain 'E' and resid 441 through 444' Processing helix chain 'E' and resid 479 through 483 Processing helix chain 'E' and resid 495 through 504 removed outlier: 4.863A pdb=" N ASN E 500 " --> pdb=" O ASP E 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 511 Processing helix chain 'E' and resid 525 through 534 Processing helix chain 'E' and resid 542 through 560 Processing helix chain 'E' and resid 632 through 648 removed outlier: 3.589A pdb=" N ARG E 648 " --> pdb=" O VAL E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 658 through 661 No H-bonds generated for 'chain 'E' and resid 658 through 661' Processing helix chain 'E' and resid 681 through 693 Processing helix chain 'E' and resid 719 through 727 Processing helix chain 'E' and resid 742 through 744 No H-bonds generated for 'chain 'E' and resid 742 through 744' Processing helix chain 'E' and resid 749 through 754 Processing helix chain 'E' and resid 763 through 769 Processing helix chain 'F' and resid 255 through 261 removed outlier: 3.542A pdb=" N ALA F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 279 Processing helix chain 'F' and resid 286 through 300 removed outlier: 3.829A pdb=" N MET F 298 " --> pdb=" O TYR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 322 removed outlier: 4.289A pdb=" N THR F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 343 Processing helix chain 'F' and resid 363 through 373 removed outlier: 3.665A pdb=" N SER F 368 " --> pdb=" O SER F 364 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 413 Processing helix chain 'F' and resid 441 through 444 No H-bonds generated for 'chain 'F' and resid 441 through 444' Processing helix chain 'F' and resid 479 through 484 removed outlier: 3.887A pdb=" N ASP F 483 " --> pdb=" O ALA F 479 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 479 through 484' Processing helix chain 'F' and resid 495 through 505 Processing helix chain 'F' and resid 507 through 511 Processing helix chain 'F' and resid 525 through 535 Processing helix chain 'F' and resid 542 through 560 Processing helix chain 'F' and resid 576 through 579 No H-bonds generated for 'chain 'F' and resid 576 through 579' Processing helix chain 'F' and resid 635 through 648 removed outlier: 3.543A pdb=" N ARG F 648 " --> pdb=" O VAL F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 658 through 661 No H-bonds generated for 'chain 'F' and resid 658 through 661' Processing helix chain 'F' and resid 682 through 693 Processing helix chain 'F' and resid 719 through 728 Processing helix chain 'F' and resid 741 through 744 No H-bonds generated for 'chain 'F' and resid 741 through 744' Processing helix chain 'F' and resid 749 through 754 removed outlier: 4.404A pdb=" N ASP F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 763 through 769 removed outlier: 3.836A pdb=" N ILE F 769 " --> pdb=" O ASP F 765 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 485 through 490 removed outlier: 6.396A pdb=" N ILE A 351 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE A 488 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS A 353 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 490 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 355 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 356 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 469 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 521 through 523 removed outlier: 6.718A pdb=" N ILE A 568 " --> pdb=" O THR A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 614 through 619 Processing sheet with id= D, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.590A pdb=" N VAL A 733 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU A 756 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE A 736 " --> pdb=" O GLU A 756 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N HIS A 758 " --> pdb=" O ILE A 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 485 through 489 removed outlier: 6.346A pdb=" N ILE B 351 " --> pdb=" O GLU B 486 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 488 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N CYS B 353 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B 352 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET B 467 " --> pdb=" O PRO B 418 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL B 469 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLN B 376 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU B 421 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 378 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP B 423 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET B 380 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 598 through 604 Processing sheet with id= G, first strand: chain 'B' and resid 614 through 619 removed outlier: 3.567A pdb=" N THR B 627 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 701 through 703 removed outlier: 7.256A pdb=" N VAL B 733 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS B 758 " --> pdb=" O ILE B 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 485 through 490 removed outlier: 6.257A pdb=" N ILE C 351 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE C 488 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N CYS C 353 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C 490 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL C 355 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 356 " --> pdb=" O SER C 472 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 376 through 378 removed outlier: 3.562A pdb=" N VAL C 378 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 521 through 523 removed outlier: 6.916A pdb=" N ILE C 568 " --> pdb=" O THR C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 597 through 602 removed outlier: 3.715A pdb=" N VAL C 668 " --> pdb=" O THR C 627 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.761A pdb=" N VAL C 733 " --> pdb=" O ALA C 702 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 352 through 355 removed outlier: 4.270A pdb=" N LEU D 352 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA D 470 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 354 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 472 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 598 through 602 removed outlier: 3.884A pdb=" N ASP D 609 " --> pdb=" O ALA D 602 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 627 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL D 668 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 701 through 703 removed outlier: 6.727A pdb=" N VAL D 733 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU D 756 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE D 736 " --> pdb=" O GLU D 756 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS D 758 " --> pdb=" O ILE D 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 485 through 490 removed outlier: 6.214A pdb=" N ILE E 351 " --> pdb=" O GLU E 486 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE E 488 " --> pdb=" O ILE E 351 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS E 353 " --> pdb=" O ILE E 488 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU E 490 " --> pdb=" O CYS E 353 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL E 355 " --> pdb=" O LEU E 490 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU E 352 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY E 356 " --> pdb=" O SER E 472 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL E 469 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 422 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL E 378 " --> pdb=" O LEU E 421 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 521 through 523 removed outlier: 6.852A pdb=" N ILE E 568 " --> pdb=" O THR E 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 597 through 602 removed outlier: 3.544A pdb=" N ILE E 613 " --> pdb=" O VAL E 598 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 602 " --> pdb=" O ASP E 609 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP E 609 " --> pdb=" O ALA E 602 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 668 " --> pdb=" O THR E 627 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 701 through 703 removed outlier: 6.276A pdb=" N VAL E 733 " --> pdb=" O ALA E 702 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU E 756 " --> pdb=" O VAL E 734 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE E 736 " --> pdb=" O GLU E 756 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N HIS E 758 " --> pdb=" O ILE E 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 485 through 490 removed outlier: 6.063A pdb=" N ILE F 351 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE F 488 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS F 353 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU F 490 " --> pdb=" O CYS F 353 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL F 355 " --> pdb=" O LEU F 490 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU F 352 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY F 356 " --> pdb=" O SER F 472 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL F 469 " --> pdb=" O PHE F 420 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 521 through 523 removed outlier: 6.637A pdb=" N ILE F 568 " --> pdb=" O THR F 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 597 through 603 removed outlier: 3.682A pdb=" N HIS F 665 " --> pdb=" O ALA F 616 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 701 through 703 removed outlier: 6.606A pdb=" N VAL F 733 " --> pdb=" O ALA F 702 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS F 758 " --> pdb=" O ILE F 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= X 721 hydrogen bonds defined for protein. 2085 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: 6.83 Time building geometry restraints manager: 8.91 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: 5497 1.33 - 1.45: 3621 1.45 - 1.57: 13586 1.57 - 1.69: 15 1.69 - 1.81: 216 Bond restraints: 22935 Sorted by residual: bond pdb=" CA ILE C 638 " pdb=" C ILE C 638 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.27e-02 6.20e+03 1.77e+01 bond pdb=" CA MET C 634 " pdb=" C MET C 634 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.36e-02 5.41e+03 1.31e+01 bond pdb=" CA ILE C 638 " pdb=" CB ILE C 638 " ideal model delta sigma weight residual 1.540 1.498 0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" N MET C 634 " pdb=" CA MET C 634 " ideal model delta sigma weight residual 1.459 1.419 0.040 1.25e-02 6.40e+03 1.03e+01 bond pdb=" N ALA C 640 " pdb=" CA ALA C 640 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.21e-02 6.83e+03 7.83e+00 ... (remaining 22930 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.83: 514 104.83 - 112.74: 12587 112.74 - 120.65: 10601 120.65 - 128.56: 7132 128.56 - 136.47: 125 Bond angle restraints: 30959 Sorted by residual: angle pdb=" N GLU C 632 " pdb=" CA GLU C 632 " pdb=" C GLU C 632 " ideal model delta sigma weight residual 111.07 119.22 -8.15 1.07e+00 8.73e-01 5.80e+01 angle pdb=" O VAL C 633 " pdb=" C VAL C 633 " pdb=" N MET C 634 " ideal model delta sigma weight residual 121.87 127.45 -5.58 1.01e+00 9.80e-01 3.05e+01 angle pdb=" CA VAL C 633 " pdb=" C VAL C 633 " pdb=" N MET C 634 " ideal model delta sigma weight residual 117.53 111.25 6.28 1.19e+00 7.06e-01 2.78e+01 angle pdb=" N SER C 629 " pdb=" CA SER C 629 " pdb=" C SER C 629 " ideal model delta sigma weight residual 110.53 117.39 -6.86 1.32e+00 5.74e-01 2.70e+01 angle pdb=" C ALA C 640 " pdb=" N ALA C 641 " pdb=" CA ALA C 641 " ideal model delta sigma weight residual 120.28 113.32 6.96 1.34e+00 5.57e-01 2.70e+01 ... (remaining 30954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.19: 13815 23.19 - 46.38: 436 46.38 - 69.57: 24 69.57 - 92.76: 6 92.76 - 115.94: 1 Dihedral angle restraints: 14282 sinusoidal: 5925 harmonic: 8357 Sorted by residual: dihedral pdb=" O1B ADP A 800 " pdb=" O3A ADP A 800 " pdb=" PB ADP A 800 " pdb=" PA ADP A 800 " ideal model delta sinusoidal sigma weight residual -60.00 55.94 -115.94 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" CA LYS A 517 " pdb=" C LYS A 517 " pdb=" N LYS A 518 " pdb=" CA LYS A 518 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PRO A 678 " pdb=" C PRO A 678 " pdb=" N SER A 679 " pdb=" CA SER A 679 " ideal model delta harmonic sigma weight residual 180.00 152.95 27.05 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 14279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2842 0.075 - 0.149: 728 0.149 - 0.224: 56 0.224 - 0.299: 4 0.299 - 0.373: 1 Chirality restraints: 3631 Sorted by residual: chirality pdb=" CA MET C 634 " pdb=" N MET C 634 " pdb=" C MET C 634 " pdb=" CB MET C 634 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CG LEU B 365 " pdb=" CB LEU B 365 " pdb=" CD1 LEU B 365 " pdb=" CD2 LEU B 365 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB VAL B 606 " pdb=" CA VAL B 606 " pdb=" CG1 VAL B 606 " pdb=" CG2 VAL B 606 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.26 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3628 not shown) Planarity restraints: 3938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 507 " 0.048 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO B 508 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 508 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 508 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 507 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO D 508 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 508 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 508 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 507 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO E 508 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 508 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 508 " -0.036 5.00e-02 4.00e+02 ... (remaining 3935 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4831 2.77 - 3.31: 20767 3.31 - 3.84: 36104 3.84 - 4.37: 41244 4.37 - 4.90: 69139 Nonbonded interactions: 172085 Sorted by model distance: nonbonded pdb=" OG1 THR B 536 " pdb=" OE1 GLU B 538 " model vdw 2.243 2.440 nonbonded pdb=" OD1 ASP E 423 " pdb=" OG1 THR E 471 " model vdw 2.253 2.440 nonbonded pdb=" O ALA E 267 " pdb=" OG1 THR E 271 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR F 363 " pdb=" O3B ADP F 800 " model vdw 2.262 2.440 nonbonded pdb=" O VAL B 595 " pdb=" OG SER B 690 " model vdw 2.267 2.440 ... (remaining 172080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 253 through 300 or resid 316 through 380 or resid 404 thro \ ugh 426 or resid 437 through 448 or resid 464 through 532 or resid 534 through 5 \ 60 or resid 566 through 579 or resid 597 through 674 or resid 678 through 685 or \ (resid 686 and (name N or name CA or name C or name O )) or resid 687 through 7 \ 75)) selection = (chain 'B' and (resid 253 through 280 or resid 288 through 300 or resid 316 thro \ ugh 380 or resid 404 through 426 or resid 437 through 448 or resid 464 through 5 \ 32 or resid 534 through 560 or resid 566 through 579 or resid 597 through 674 or \ resid 678 through 685 or (resid 686 and (name N or name CA or name C or name O \ )) or resid 687 through 775)) selection = (chain 'C' and (resid 253 through 280 or resid 288 through 300 or resid 316 thro \ ugh 380 or resid 404 through 426 or resid 437 through 448 or resid 464 through 5 \ 60 or resid 566 through 579 or resid 597 through 674 or resid 678 through 685 or \ (resid 686 and (name N or name CA or name C or name O )) or resid 687 through 7 \ 75)) selection = (chain 'D' and (resid 253 through 280 or resid 288 through 300 or resid 316 thro \ ugh 380 or resid 404 through 448 or resid 464 through 532 or resid 534 through 6 \ 74 or resid 678 through 685 or (resid 686 and (name N or name CA or name C or na \ me O )) or resid 687 through 775)) selection = (chain 'E' and (resid 253 through 280 or resid 288 through 380 or resid 404 thro \ ugh 426 or resid 437 through 532 or resid 534 through 560 or resid 566 through 5 \ 79 or resid 597 through 674 or resid 678 through 685 or (resid 686 and (name N o \ r name CA or name C or name O )) or resid 687 through 775)) selection = (chain 'F' and (resid 253 through 280 or resid 288 through 300 or resid 316 thro \ ugh 380 or resid 404 through 426 or resid 437 through 448 or resid 464 through 5 \ 32 or resid 534 through 560 or resid 566 through 579 or resid 597 through 775)) } 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: 1.040 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: 4.860 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 56.430 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.067 22935 Z= 0.551 Angle : 1.074 10.755 30959 Z= 0.576 Chirality : 0.062 0.373 3631 Planarity : 0.008 0.072 3938 Dihedral : 11.183 115.944 8878 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.90 % Allowed : 4.97 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.12), residues: 2857 helix: -3.49 (0.09), residues: 1209 sheet: -1.97 (0.24), residues: 403 loop : -2.67 (0.15), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 603 HIS 0.012 0.002 HIS E 727 PHE 0.020 0.003 PHE B 658 TYR 0.026 0.003 TYR A 535 ARG 0.023 0.001 ARG C 553 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 636 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7422 (tmm) cc_final: 0.6911 (tmm) REVERT: A 296 ASP cc_start: 0.8700 (m-30) cc_final: 0.8307 (m-30) REVERT: A 351 ILE cc_start: 0.7629 (mp) cc_final: 0.6931 (mm) REVERT: A 606 VAL cc_start: 0.7459 (m) cc_final: 0.7216 (t) REVERT: B 262 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7829 (tptt) REVERT: B 296 ASP cc_start: 0.8633 (m-30) cc_final: 0.8304 (m-30) REVERT: B 522 THR cc_start: 0.8969 (p) cc_final: 0.8713 (t) REVERT: C 268 ARG cc_start: 0.8433 (mtm110) cc_final: 0.7793 (ttm-80) REVERT: C 297 TRP cc_start: 0.8739 (m100) cc_final: 0.7533 (m100) REVERT: C 426 ASP cc_start: 0.7655 (t0) cc_final: 0.7441 (t0) REVERT: C 529 MET cc_start: 0.8254 (mmm) cc_final: 0.8015 (tpt) REVERT: D 270 LYS cc_start: 0.8880 (mmpt) cc_final: 0.8619 (pttt) REVERT: D 294 TYR cc_start: 0.7375 (t80) cc_final: 0.6097 (m-10) REVERT: D 336 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7094 (mt-10) REVERT: D 728 ARG cc_start: 0.7423 (ttp-110) cc_final: 0.7088 (ttp80) REVERT: E 280 MET cc_start: 0.6455 (mtt) cc_final: 0.5675 (mmm) REVERT: E 333 ARG cc_start: 0.8186 (tpt170) cc_final: 0.7791 (ttt180) REVERT: E 354 LEU cc_start: 0.8684 (mt) cc_final: 0.8387 (mp) REVERT: E 516 ILE cc_start: 0.8186 (mt) cc_final: 0.7934 (mm) REVERT: E 609 ASP cc_start: 0.9217 (p0) cc_final: 0.8869 (p0) REVERT: E 633 VAL cc_start: 0.7706 (t) cc_final: 0.7074 (p) REVERT: F 380 MET cc_start: 0.7959 (tpt) cc_final: 0.7530 (tpp) REVERT: F 456 TYR cc_start: 0.6963 (t80) cc_final: 0.6617 (m-80) outliers start: 22 outliers final: 8 residues processed: 651 average time/residue: 0.3877 time to fit residues: 369.6506 Evaluate side-chains 351 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 343 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 629 SER Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 168 optimal weight: 0.0270 chunk 262 optimal weight: 0.9980 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 ASN B 500 ASN B 758 HIS ** C 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 476 ASN C 510 GLN C 514 ASN C 758 HIS D 276 GLN D 476 ASN ** E 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 571 ASN E 635 GLN F 448 GLN F 500 ASN F 514 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22935 Z= 0.187 Angle : 0.686 9.797 30959 Z= 0.341 Chirality : 0.045 0.185 3631 Planarity : 0.006 0.056 3938 Dihedral : 7.558 113.319 3187 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.65 % Allowed : 12.35 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.14), residues: 2857 helix: -1.85 (0.13), residues: 1222 sheet: -1.36 (0.25), residues: 406 loop : -2.18 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 603 HIS 0.007 0.001 HIS B 665 PHE 0.010 0.001 PHE E 468 TYR 0.024 0.002 TYR C 626 ARG 0.005 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 409 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 VAL cc_start: 0.8730 (t) cc_final: 0.8407 (t) REVERT: B 262 LYS cc_start: 0.8283 (ttpt) cc_final: 0.7916 (tptt) REVERT: B 281 MET cc_start: 0.6952 (ptt) cc_final: 0.6713 (ptt) REVERT: B 296 ASP cc_start: 0.8618 (m-30) cc_final: 0.8327 (m-30) REVERT: B 467 MET cc_start: 0.7036 (ttt) cc_final: 0.6796 (mtp) REVERT: B 522 THR cc_start: 0.8823 (p) cc_final: 0.8534 (t) REVERT: B 626 TYR cc_start: 0.6234 (m-80) cc_final: 0.5911 (m-10) REVERT: B 632 GLU cc_start: 0.7381 (mp0) cc_final: 0.7095 (mp0) REVERT: C 297 TRP cc_start: 0.8577 (m100) cc_final: 0.7660 (m100) REVERT: C 419 LEU cc_start: 0.9343 (tt) cc_final: 0.9135 (tt) REVERT: C 529 MET cc_start: 0.8348 (mmm) cc_final: 0.8107 (tpt) REVERT: C 615 THR cc_start: 0.9075 (p) cc_final: 0.8852 (p) REVERT: D 297 TRP cc_start: 0.7018 (m100) cc_final: 0.6242 (m-10) REVERT: D 336 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7408 (mp0) REVERT: E 280 MET cc_start: 0.6346 (mtt) cc_final: 0.5683 (ptt) REVERT: E 354 LEU cc_start: 0.8597 (mt) cc_final: 0.8308 (mp) REVERT: E 609 ASP cc_start: 0.9162 (p0) cc_final: 0.8817 (p0) REVERT: F 271 THR cc_start: 0.9114 (m) cc_final: 0.8721 (t) REVERT: F 441 LEU cc_start: 0.8294 (pt) cc_final: 0.7839 (tp) REVERT: F 456 TYR cc_start: 0.7223 (t80) cc_final: 0.6569 (m-80) outliers start: 65 outliers final: 37 residues processed: 458 average time/residue: 0.3343 time to fit residues: 236.2882 Evaluate side-chains 344 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 307 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 690 SER Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 300 GLN Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 262 optimal weight: 6.9990 chunk 284 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS A 408 GLN A 582 GLN C 448 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN D 476 ASN E 514 ASN E 597 GLN E 635 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 514 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22935 Z= 0.327 Angle : 0.725 12.601 30959 Z= 0.355 Chirality : 0.046 0.188 3631 Planarity : 0.005 0.048 3938 Dihedral : 7.375 113.155 3182 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.79 % Allowed : 14.11 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.15), residues: 2857 helix: -1.12 (0.14), residues: 1231 sheet: -1.26 (0.25), residues: 395 loop : -1.99 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 603 HIS 0.006 0.001 HIS C 324 PHE 0.017 0.001 PHE A 452 TYR 0.021 0.002 TYR D 294 ARG 0.005 0.001 ARG D 728 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 308 time to evaluate : 2.722 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: A 615 THR cc_start: 0.8882 (p) cc_final: 0.8614 (p) REVERT: B 262 LYS cc_start: 0.8282 (ttpt) cc_final: 0.7796 (tptt) REVERT: B 265 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8534 (mmmt) REVERT: B 296 ASP cc_start: 0.8786 (m-30) cc_final: 0.8504 (m-30) REVERT: B 467 MET cc_start: 0.6838 (ttt) cc_final: 0.6580 (mtp) REVERT: B 632 GLU cc_start: 0.7422 (mp0) cc_final: 0.7203 (mp0) REVERT: C 276 GLN cc_start: 0.7547 (pp30) cc_final: 0.7272 (tp40) REVERT: C 297 TRP cc_start: 0.8742 (m100) cc_final: 0.7724 (m100) REVERT: C 529 MET cc_start: 0.8418 (mmm) cc_final: 0.8128 (tpt) REVERT: C 615 THR cc_start: 0.9083 (p) cc_final: 0.8848 (p) REVERT: D 336 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7608 (mp0) REVERT: D 716 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8646 (tp) REVERT: E 280 MET cc_start: 0.6255 (mtt) cc_final: 0.5550 (ptt) REVERT: E 354 LEU cc_start: 0.8724 (mt) cc_final: 0.8416 (mp) REVERT: E 635 GLN cc_start: 0.8604 (mt0) cc_final: 0.8135 (tm-30) REVERT: F 402 MET cc_start: 0.6385 (tpt) cc_final: 0.5752 (pmm) REVERT: F 456 TYR cc_start: 0.7294 (t80) cc_final: 0.6850 (m-80) outliers start: 93 outliers final: 65 residues processed: 379 average time/residue: 0.3188 time to fit residues: 190.1706 Evaluate side-chains 329 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 263 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 265 LYS Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 300 GLN Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 chunk 125 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN C 473 ASN D 476 ASN ** D 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22935 Z= 0.201 Angle : 0.644 10.372 30959 Z= 0.314 Chirality : 0.044 0.168 3631 Planarity : 0.004 0.042 3938 Dihedral : 7.055 112.075 3182 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.38 % Allowed : 15.74 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.15), residues: 2857 helix: -0.60 (0.15), residues: 1210 sheet: -1.21 (0.26), residues: 393 loop : -1.70 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 603 HIS 0.004 0.001 HIS E 667 PHE 0.018 0.001 PHE F 452 TYR 0.023 0.001 TYR E 626 ARG 0.005 0.000 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 302 time to evaluate : 2.612 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 262 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7846 (tptt) REVERT: B 296 ASP cc_start: 0.8708 (m-30) cc_final: 0.8375 (m-30) REVERT: B 321 ASP cc_start: 0.8231 (m-30) cc_final: 0.7800 (t0) REVERT: B 522 THR cc_start: 0.8942 (p) cc_final: 0.8632 (t) REVERT: C 297 TRP cc_start: 0.8735 (m100) cc_final: 0.7758 (m100) REVERT: C 529 MET cc_start: 0.8354 (mmm) cc_final: 0.8077 (tpt) REVERT: D 298 MET cc_start: 0.8157 (mmp) cc_final: 0.7824 (mmt) REVERT: D 336 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7503 (mp0) REVERT: D 716 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8660 (tp) REVERT: E 280 MET cc_start: 0.5987 (mtt) cc_final: 0.5325 (ptt) REVERT: E 354 LEU cc_start: 0.8704 (mt) cc_final: 0.8396 (mp) REVERT: E 615 THR cc_start: 0.8590 (p) cc_final: 0.8333 (p) REVERT: E 636 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8009 (mp0) outliers start: 83 outliers final: 61 residues processed: 363 average time/residue: 0.3135 time to fit residues: 181.2502 Evaluate side-chains 327 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 264 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 265 LYS Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 453 ASN Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN D 476 ASN ** D 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22935 Z= 0.244 Angle : 0.653 11.598 30959 Z= 0.318 Chirality : 0.045 0.315 3631 Planarity : 0.004 0.042 3938 Dihedral : 6.947 111.802 3182 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.91 % Allowed : 16.18 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.15), residues: 2857 helix: -0.38 (0.15), residues: 1217 sheet: -1.09 (0.25), residues: 403 loop : -1.65 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 603 HIS 0.004 0.001 HIS C 324 PHE 0.015 0.001 PHE A 452 TYR 0.015 0.001 TYR E 626 ARG 0.007 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 275 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.5423 (ppp) cc_final: 0.4972 (ppp) REVERT: B 262 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7796 (tptt) REVERT: B 265 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8586 (mmmt) REVERT: B 321 ASP cc_start: 0.8234 (m-30) cc_final: 0.7806 (t0) REVERT: B 467 MET cc_start: 0.7130 (mtp) cc_final: 0.6170 (mtp) REVERT: B 522 THR cc_start: 0.8970 (p) cc_final: 0.8664 (t) REVERT: C 297 TRP cc_start: 0.8762 (m100) cc_final: 0.7966 (m100) REVERT: C 529 MET cc_start: 0.8435 (mmm) cc_final: 0.8104 (tpt) REVERT: D 298 MET cc_start: 0.8176 (mmp) cc_final: 0.7950 (mmt) REVERT: D 336 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7632 (mp0) REVERT: D 716 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8625 (tp) REVERT: E 280 MET cc_start: 0.6004 (mtt) cc_final: 0.5276 (ptt) REVERT: E 354 LEU cc_start: 0.8663 (mt) cc_final: 0.8336 (mp) REVERT: E 615 THR cc_start: 0.8631 (p) cc_final: 0.8405 (p) REVERT: F 380 MET cc_start: 0.7629 (tpp) cc_final: 0.7326 (tpp) outliers start: 96 outliers final: 73 residues processed: 344 average time/residue: 0.2998 time to fit residues: 165.7118 Evaluate side-chains 335 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 261 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 453 ASN Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 265 LYS Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 453 ASN Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 4.9990 chunk 251 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 279 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN D 476 ASN ** D 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22935 Z= 0.186 Angle : 0.631 14.400 30959 Z= 0.304 Chirality : 0.044 0.346 3631 Planarity : 0.004 0.043 3938 Dihedral : 6.770 112.043 3182 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.63 % Allowed : 16.96 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.16), residues: 2857 helix: -0.21 (0.15), residues: 1220 sheet: -0.97 (0.26), residues: 403 loop : -1.57 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 603 HIS 0.004 0.001 HIS F 324 PHE 0.011 0.001 PHE C 420 TYR 0.014 0.001 TYR F 294 ARG 0.006 0.000 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 284 time to evaluate : 2.679 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: A 263 MET cc_start: 0.6662 (tmm) cc_final: 0.6404 (tmm) REVERT: A 402 MET cc_start: 0.5497 (ppp) cc_final: 0.4987 (ppp) REVERT: B 262 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7765 (tptt) REVERT: B 321 ASP cc_start: 0.8199 (m-30) cc_final: 0.7795 (t0) REVERT: B 380 MET cc_start: 0.7729 (tpt) cc_final: 0.7334 (tpt) REVERT: B 449 ASN cc_start: 0.8116 (m-40) cc_final: 0.7776 (m-40) REVERT: B 467 MET cc_start: 0.7004 (mtp) cc_final: 0.6061 (mtp) REVERT: B 522 THR cc_start: 0.8941 (p) cc_final: 0.8640 (t) REVERT: C 297 TRP cc_start: 0.8764 (m100) cc_final: 0.8040 (m100) REVERT: C 529 MET cc_start: 0.8409 (mmm) cc_final: 0.8093 (tpt) REVERT: D 336 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7614 (mp0) REVERT: D 716 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8610 (tp) REVERT: E 280 MET cc_start: 0.5910 (mtt) cc_final: 0.5073 (ptm) REVERT: E 354 LEU cc_start: 0.8642 (mt) cc_final: 0.8321 (mp) REVERT: E 588 ARG cc_start: 0.6071 (ptt180) cc_final: 0.5829 (ptt180) REVERT: E 615 THR cc_start: 0.8587 (p) cc_final: 0.8379 (p) outliers start: 89 outliers final: 67 residues processed: 352 average time/residue: 0.3036 time to fit residues: 172.6410 Evaluate side-chains 325 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 257 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 453 ASN Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 265 LYS Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 453 ASN Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 476 ASN B 667 HIS D 476 ASN ** D 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 22935 Z= 0.420 Angle : 0.774 10.941 30959 Z= 0.377 Chirality : 0.048 0.302 3631 Planarity : 0.005 0.044 3938 Dihedral : 7.224 113.917 3182 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.91 % Allowed : 17.33 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2857 helix: -0.41 (0.15), residues: 1222 sheet: -0.94 (0.26), residues: 381 loop : -1.65 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 603 HIS 0.008 0.001 HIS C 324 PHE 0.017 0.002 PHE F 452 TYR 0.017 0.002 TYR D 294 ARG 0.004 0.001 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 265 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.5323 (ppp) cc_final: 0.4915 (ppp) REVERT: B 262 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7558 (tptt) REVERT: B 321 ASP cc_start: 0.8306 (m-30) cc_final: 0.7903 (t0) REVERT: B 609 ASP cc_start: 0.8021 (t0) cc_final: 0.7811 (t0) REVERT: C 529 MET cc_start: 0.8473 (mmm) cc_final: 0.8153 (tpt) REVERT: C 615 THR cc_start: 0.9176 (p) cc_final: 0.8942 (p) REVERT: D 336 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7748 (mp0) REVERT: D 716 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8640 (tp) REVERT: E 280 MET cc_start: 0.5511 (mtt) cc_final: 0.4701 (ptm) REVERT: E 354 LEU cc_start: 0.8679 (mt) cc_final: 0.8437 (mp) REVERT: E 477 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8651 (tp) REVERT: E 588 ARG cc_start: 0.6133 (ptt180) cc_final: 0.5874 (ptt180) REVERT: E 615 THR cc_start: 0.8741 (p) cc_final: 0.8533 (p) outliers start: 96 outliers final: 78 residues processed: 341 average time/residue: 0.3255 time to fit residues: 179.0404 Evaluate side-chains 332 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 252 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 453 ASN Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 634 MET Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 265 LYS Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 682 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 9.9990 chunk 111 optimal weight: 0.0870 chunk 166 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 25 optimal weight: 0.0070 chunk 218 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 476 ASN D 476 ASN ** D 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22935 Z= 0.161 Angle : 0.642 11.392 30959 Z= 0.309 Chirality : 0.044 0.292 3631 Planarity : 0.004 0.042 3938 Dihedral : 6.728 112.426 3182 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.98 % Allowed : 18.79 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.16), residues: 2857 helix: 0.07 (0.16), residues: 1203 sheet: -0.83 (0.26), residues: 411 loop : -1.43 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 603 HIS 0.003 0.001 HIS E 665 PHE 0.019 0.001 PHE F 452 TYR 0.017 0.001 TYR F 294 ARG 0.003 0.000 ARG F 484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 295 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.6816 (tmm) cc_final: 0.6207 (tmm) REVERT: A 402 MET cc_start: 0.5551 (ppp) cc_final: 0.5153 (ppp) REVERT: B 262 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7585 (tptt) REVERT: B 321 ASP cc_start: 0.8140 (m-30) cc_final: 0.7790 (t0) REVERT: B 380 MET cc_start: 0.7711 (tpt) cc_final: 0.7384 (tpt) REVERT: B 449 ASN cc_start: 0.8152 (m-40) cc_final: 0.7795 (m-40) REVERT: B 467 MET cc_start: 0.7021 (mtp) cc_final: 0.6664 (mtp) REVERT: B 522 THR cc_start: 0.8967 (p) cc_final: 0.8679 (t) REVERT: C 263 MET cc_start: 0.7708 (mmm) cc_final: 0.7378 (mpp) REVERT: C 297 TRP cc_start: 0.8832 (m100) cc_final: 0.8432 (m100) REVERT: C 529 MET cc_start: 0.8387 (mmm) cc_final: 0.8083 (tpt) REVERT: C 615 THR cc_start: 0.9148 (p) cc_final: 0.8901 (p) REVERT: D 336 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7549 (mp0) REVERT: D 716 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8628 (tp) REVERT: E 280 MET cc_start: 0.5752 (mtt) cc_final: 0.5242 (ptm) REVERT: E 477 ILE cc_start: 0.8849 (mp) cc_final: 0.8637 (tp) REVERT: E 615 THR cc_start: 0.8601 (p) cc_final: 0.8388 (p) outliers start: 73 outliers final: 53 residues processed: 349 average time/residue: 0.3121 time to fit residues: 174.7606 Evaluate side-chains 318 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 264 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 453 ASN Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 529 MET Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 703 MET Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 265 LYS Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 6.9990 chunk 266 optimal weight: 0.2980 chunk 243 optimal weight: 20.0000 chunk 259 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 203 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 245 optimal weight: 8.9990 chunk 258 optimal weight: 9.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 417 ASN D 476 ASN ** D 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22935 Z= 0.361 Angle : 0.747 13.711 30959 Z= 0.361 Chirality : 0.048 0.341 3631 Planarity : 0.004 0.042 3938 Dihedral : 7.000 113.471 3182 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.42 % Allowed : 19.12 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2857 helix: -0.04 (0.15), residues: 1202 sheet: -0.80 (0.27), residues: 385 loop : -1.59 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 603 HIS 0.007 0.001 HIS C 324 PHE 0.013 0.001 PHE C 420 TYR 0.015 0.002 TYR E 325 ARG 0.012 0.001 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 255 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.5401 (ppp) cc_final: 0.4980 (ppp) REVERT: B 321 ASP cc_start: 0.8303 (m-30) cc_final: 0.7928 (t0) REVERT: B 380 MET cc_start: 0.7840 (tpt) cc_final: 0.7476 (tpt) REVERT: B 449 ASN cc_start: 0.8082 (m-40) cc_final: 0.7678 (m-40) REVERT: B 467 MET cc_start: 0.7218 (mtp) cc_final: 0.6797 (mtp) REVERT: C 529 MET cc_start: 0.8496 (mmm) cc_final: 0.8151 (tpt) REVERT: C 538 GLU cc_start: 0.6759 (pt0) cc_final: 0.6414 (pt0) REVERT: C 615 THR cc_start: 0.9120 (p) cc_final: 0.8895 (p) REVERT: D 336 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7702 (mp0) REVERT: D 716 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8638 (tp) REVERT: E 280 MET cc_start: 0.5837 (mtt) cc_final: 0.5194 (ptt) outliers start: 84 outliers final: 71 residues processed: 318 average time/residue: 0.3165 time to fit residues: 161.1358 Evaluate side-chains 314 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 242 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 453 ASN Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 501 ILE Chi-restraints excluded: chain E residue 529 MET Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 634 MET Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 750 ASN Chi-restraints excluded: chain F residue 265 LYS Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 5.9990 chunk 274 optimal weight: 6.9990 chunk 167 optimal weight: 0.0040 chunk 130 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 287 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 476 ASN ** D 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN F 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22935 Z= 0.269 Angle : 0.705 11.149 30959 Z= 0.339 Chirality : 0.046 0.239 3631 Planarity : 0.004 0.042 3938 Dihedral : 6.950 113.516 3182 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.81 % Allowed : 19.77 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.16), residues: 2857 helix: 0.01 (0.15), residues: 1206 sheet: -0.79 (0.26), residues: 401 loop : -1.58 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 603 HIS 0.005 0.001 HIS C 324 PHE 0.020 0.001 PHE F 452 TYR 0.013 0.001 TYR A 626 ARG 0.005 0.000 ARG C 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 257 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.5402 (ppp) cc_final: 0.5011 (ppp) REVERT: B 262 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7546 (tptt) REVERT: B 296 ASP cc_start: 0.8681 (m-30) cc_final: 0.8124 (p0) REVERT: B 321 ASP cc_start: 0.8215 (m-30) cc_final: 0.7864 (t0) REVERT: B 336 GLU cc_start: 0.7644 (tt0) cc_final: 0.7436 (tt0) REVERT: B 380 MET cc_start: 0.7804 (tpt) cc_final: 0.7489 (tpt) REVERT: B 449 ASN cc_start: 0.8119 (m-40) cc_final: 0.7776 (m-40) REVERT: B 467 MET cc_start: 0.7303 (mtp) cc_final: 0.6859 (mtp) REVERT: C 263 MET cc_start: 0.7857 (mmm) cc_final: 0.7505 (mpp) REVERT: C 476 ASN cc_start: 0.8648 (t0) cc_final: 0.8268 (t0) REVERT: C 529 MET cc_start: 0.8456 (mmm) cc_final: 0.8130 (tpt) REVERT: C 615 THR cc_start: 0.9117 (p) cc_final: 0.8883 (p) REVERT: D 336 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7643 (mp0) REVERT: D 493 TYR cc_start: 0.7512 (m-80) cc_final: 0.7033 (m-80) REVERT: D 716 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8617 (tp) REVERT: E 280 MET cc_start: 0.5734 (mtt) cc_final: 0.5527 (mmp) outliers start: 69 outliers final: 64 residues processed: 311 average time/residue: 0.3049 time to fit residues: 151.9232 Evaluate side-chains 311 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 246 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 453 ASN Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 501 ILE Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 750 ASN Chi-restraints excluded: chain F residue 265 LYS Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 182 optimal weight: 0.0470 chunk 244 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 211 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 229 optimal weight: 7.9990 chunk 96 optimal weight: 0.0770 chunk 235 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS D 476 ASN ** D 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.121878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.097076 restraints weight = 57699.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099953 restraints weight = 29748.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.101794 restraints weight = 18947.511| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22935 Z= 0.167 Angle : 0.662 11.602 30959 Z= 0.314 Chirality : 0.045 0.262 3631 Planarity : 0.004 0.041 3938 Dihedral : 6.601 111.230 3182 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.61 % Allowed : 20.06 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2857 helix: 0.23 (0.16), residues: 1200 sheet: -0.60 (0.26), residues: 398 loop : -1.38 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 297 HIS 0.003 0.001 HIS E 665 PHE 0.012 0.001 PHE A 452 TYR 0.019 0.001 TYR D 377 ARG 0.003 0.000 ARG A 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4566.76 seconds wall clock time: 84 minutes 2.16 seconds (5042.16 seconds total)