Starting phenix.real_space_refine on Thu Feb 15 10:22:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p47_20245/02_2024/6p47_20245.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p47_20245/02_2024/6p47_20245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p47_20245/02_2024/6p47_20245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p47_20245/02_2024/6p47_20245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p47_20245/02_2024/6p47_20245.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p47_20245/02_2024/6p47_20245.pdb" } resolution = 3.9 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= 0.003 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: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 7872 2.51 5 N 1928 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 48": "NH1" <-> "NH2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A ARG 542": "NH1" <-> "NH2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A ARG 808": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 542": "NH1" <-> "NH2" Residue "B GLU 595": "OE1" <-> "OE2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B ARG 701": "NH1" <-> "NH2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "B ARG 808": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11972 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5986 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 693} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5986 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 693} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 6.61, per 1000 atoms: 0.55 Number of scatterers: 11972 At special positions: 0 Unit cell: (83.661, 119.667, 116.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 2090 8.00 N 1928 7.00 C 7872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.01 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.01 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 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: 4.67 Conformation dependent library (CDL) restraints added in 1.9 seconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 59.2% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.503A pdb=" N GLU A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.991A pdb=" N TYR A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.635A pdb=" N ILE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.814A pdb=" N LEU A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.739A pdb=" N ILE A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 327 removed outlier: 4.014A pdb=" N GLN A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.690A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 376 removed outlier: 4.432A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 376 " --> pdb=" O CYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 401 removed outlier: 3.528A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 446 through 462 removed outlier: 3.730A pdb=" N SER A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 460 " --> pdb=" O CYS A 456 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 486 removed outlier: 4.131A pdb=" N ILE A 467 " --> pdb=" O TRP A 463 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 537 removed outlier: 3.631A pdb=" N MET A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 516 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 572 removed outlier: 3.537A pdb=" N TYR A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 637 removed outlier: 3.756A pdb=" N GLN A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN A 623 " --> pdb=" O TRP A 619 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Proline residue: A 628 - end of helix removed outlier: 3.826A pdb=" N MET A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.564A pdb=" N TYR A 654 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.766A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.506A pdb=" N VAL A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.715A pdb=" N LEU A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 741 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.512A pdb=" N PHE A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.591A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 834 " --> pdb=" O HIS A 830 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 868 through 880 removed outlier: 3.701A pdb=" N LEU A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.502A pdb=" N GLU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 removed outlier: 3.992A pdb=" N TYR B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.635A pdb=" N ILE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.813A pdb=" N LEU B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.740A pdb=" N ILE B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 327 removed outlier: 4.014A pdb=" N GLN B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.690A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 376 removed outlier: 4.431A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 376 " --> pdb=" O CYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 401 removed outlier: 3.527A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.730A pdb=" N SER B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B 460 " --> pdb=" O CYS B 456 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 486 removed outlier: 4.131A pdb=" N ILE B 467 " --> pdb=" O TRP B 463 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 480 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 537 removed outlier: 3.632A pdb=" N MET B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 509 " --> pdb=" O PRO B 505 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 516 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 535 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 572 removed outlier: 3.537A pdb=" N TYR B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 548 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE B 558 " --> pdb=" O LYS B 554 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 637 removed outlier: 3.755A pdb=" N GLN B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN B 623 " --> pdb=" O TRP B 619 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU B 624 " --> pdb=" O ASN B 620 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 627 " --> pdb=" O GLN B 623 " (cutoff:3.500A) Proline residue: B 628 - end of helix removed outlier: 3.826A pdb=" N MET B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 636 " --> pdb=" O ASN B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 655 removed outlier: 3.564A pdb=" N TYR B 654 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.766A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.507A pdb=" N VAL B 694 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 removed outlier: 3.715A pdb=" N LEU B 735 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.513A pdb=" N PHE B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.591A pdb=" N TRP B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 834 " --> pdb=" O HIS B 830 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 840 " --> pdb=" O LEU B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 868 Processing helix chain 'B' and resid 868 through 880 removed outlier: 3.701A pdb=" N LEU B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 876 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 877 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS B 880 " --> pdb=" O GLN B 876 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 removed outlier: 3.786A pdb=" N LEU A 146 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 190 " --> pdb=" O LEU A 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 146 removed outlier: 3.786A pdb=" N LEU B 146 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 190 " --> pdb=" O LEU B 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 524 hydrogen bonds defined for protein. 1566 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: 2.97 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3515 1.34 - 1.46: 2910 1.46 - 1.58: 5749 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 12298 Sorted by residual: bond pdb=" C LEU B 627 " pdb=" N PRO B 628 " ideal model delta sigma weight residual 1.336 1.369 -0.034 9.80e-03 1.04e+04 1.17e+01 bond pdb=" C LEU A 627 " pdb=" N PRO A 628 " ideal model delta sigma weight residual 1.336 1.369 -0.033 9.80e-03 1.04e+04 1.12e+01 bond pdb=" N PRO A 421 " pdb=" CD PRO A 421 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.01e+00 bond pdb=" N PRO B 421 " pdb=" CD PRO B 421 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 7.96e+00 bond pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 1.469 1.487 -0.018 7.40e-03 1.83e+04 6.08e+00 ... (remaining 12293 not shown) Histogram of bond angle deviations from ideal: 97.82 - 105.16: 252 105.16 - 112.50: 5822 112.50 - 119.84: 4954 119.84 - 127.18: 5487 127.18 - 134.52: 149 Bond angle restraints: 16664 Sorted by residual: angle pdb=" CA PRO A 340 " pdb=" C PRO A 340 " pdb=" N ASP A 341 " ideal model delta sigma weight residual 116.20 109.36 6.84 8.00e-01 1.56e+00 7.31e+01 angle pdb=" CA PRO B 340 " pdb=" C PRO B 340 " pdb=" N ASP B 341 " ideal model delta sigma weight residual 116.20 109.37 6.83 8.00e-01 1.56e+00 7.29e+01 angle pdb=" N LEU B 503 " pdb=" CA LEU B 503 " pdb=" C LEU B 503 " ideal model delta sigma weight residual 111.36 119.69 -8.33 1.09e+00 8.42e-01 5.84e+01 angle pdb=" N LYS A 862 " pdb=" CA LYS A 862 " pdb=" CB LYS A 862 " ideal model delta sigma weight residual 110.90 100.75 10.15 1.33e+00 5.65e-01 5.83e+01 angle pdb=" N LEU A 503 " pdb=" CA LEU A 503 " pdb=" C LEU A 503 " ideal model delta sigma weight residual 111.36 119.68 -8.32 1.09e+00 8.42e-01 5.83e+01 ... (remaining 16659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 6170 17.23 - 34.46: 824 34.46 - 51.69: 156 51.69 - 68.92: 72 68.92 - 86.15: 18 Dihedral angle restraints: 7240 sinusoidal: 2950 harmonic: 4290 Sorted by residual: dihedral pdb=" CB CYS B 349 " pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " pdb=" CB CYS B 807 " ideal model delta sinusoidal sigma weight residual -86.00 -146.80 60.80 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CB CYS A 349 " pdb=" SG CYS A 349 " pdb=" SG CYS A 807 " pdb=" CB CYS A 807 " ideal model delta sinusoidal sigma weight residual -86.00 -146.80 60.80 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CA LEU B 123 " pdb=" C LEU B 123 " pdb=" N VAL B 124 " pdb=" CA VAL B 124 " ideal model delta harmonic sigma weight residual -180.00 -151.43 -28.57 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1457 0.077 - 0.155: 282 0.155 - 0.232: 58 0.232 - 0.310: 9 0.310 - 0.387: 10 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CA THR B 504 " pdb=" N THR B 504 " pdb=" C THR B 504 " pdb=" CB THR B 504 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA THR A 504 " pdb=" N THR A 504 " pdb=" C THR A 504 " pdb=" CB THR A 504 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA ASP B 353 " pdb=" N ASP B 353 " pdb=" C ASP B 353 " pdb=" CB ASP B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 1813 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 420 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO A 421 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 420 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 421 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 421 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 421 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 340 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.67e+00 pdb=" C PRO B 340 " -0.054 2.00e-02 2.50e+03 pdb=" O PRO B 340 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP B 341 " 0.018 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3054 2.77 - 3.31: 11735 3.31 - 3.84: 20391 3.84 - 4.37: 23821 4.37 - 4.90: 37772 Nonbonded interactions: 96773 Sorted by model distance: nonbonded pdb=" O ILE A 743 " pdb=" OG1 THR A 747 " model vdw 2.243 2.440 nonbonded pdb=" O ILE B 743 " pdb=" OG1 THR B 747 " model vdw 2.244 2.440 nonbonded pdb=" O GLN B 506 " pdb=" OG SER B 510 " model vdw 2.271 2.440 nonbonded pdb=" O GLN A 506 " pdb=" OG SER A 510 " model vdw 2.271 2.440 nonbonded pdb=" O VAL A 476 " pdb=" OG SER A 480 " model vdw 2.280 2.440 ... (remaining 96768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.000 Extract box with map and model: 4.190 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 32.270 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.007 0.057 12298 Z= 0.455 Angle : 1.210 10.613 16664 Z= 0.705 Chirality : 0.072 0.387 1816 Planarity : 0.009 0.102 2066 Dihedral : 17.018 86.147 4458 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.77 % Favored : 90.66 % Rotamer: Outliers : 3.68 % Allowed : 11.50 % Favored : 84.82 % Cbeta Deviations : 0.14 % 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: -5.94 (0.15), residues: 1414 helix: -4.01 (0.10), residues: 732 sheet: -4.06 (0.44), residues: 54 loop : -3.74 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 397 HIS 0.005 0.001 HIS A 830 PHE 0.021 0.002 PHE B 231 TYR 0.034 0.002 TYR A 306 ARG 0.014 0.001 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 350 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.3007 (tmm) cc_final: 0.2506 (ttp) REVERT: A 403 GLU cc_start: 0.7830 (pt0) cc_final: 0.7386 (pt0) REVERT: A 428 ASN cc_start: 0.8229 (p0) cc_final: 0.7771 (p0) REVERT: A 463 TRP cc_start: 0.6533 (t-100) cc_final: 0.5998 (t-100) REVERT: A 558 PHE cc_start: 0.8407 (t80) cc_final: 0.7963 (t80) REVERT: A 612 ILE cc_start: 0.9048 (mt) cc_final: 0.7725 (mt) REVERT: A 621 ASN cc_start: 0.8224 (m-40) cc_final: 0.8015 (m110) REVERT: A 667 GLU cc_start: 0.7407 (mp0) cc_final: 0.7132 (mp0) REVERT: A 685 PHE cc_start: 0.8305 (t80) cc_final: 0.8094 (t80) REVERT: A 867 LYS cc_start: 0.8332 (mmtm) cc_final: 0.8100 (mmtp) REVERT: A 870 ARG cc_start: 0.7280 (ttt180) cc_final: 0.7039 (mpt180) REVERT: B 386 MET cc_start: 0.8021 (mmp) cc_final: 0.7818 (mmt) REVERT: B 463 TRP cc_start: 0.7271 (t-100) cc_final: 0.6877 (t-100) REVERT: B 467 ILE cc_start: 0.8558 (mp) cc_final: 0.8279 (mp) REVERT: B 558 PHE cc_start: 0.8037 (t80) cc_final: 0.7632 (t80) REVERT: B 616 LYS cc_start: 0.9221 (tptt) cc_final: 0.8705 (tptp) REVERT: B 685 PHE cc_start: 0.8448 (t80) cc_final: 0.8187 (t80) REVERT: B 867 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8484 (mmmm) outliers start: 48 outliers final: 14 residues processed: 384 average time/residue: 0.2521 time to fit residues: 136.0157 Evaluate side-chains 276 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 262 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 865 LYS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 865 LYS Chi-restraints excluded: chain B residue 875 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 143 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 740 ASN A 830 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN B 655 HIS B 740 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12298 Z= 0.242 Angle : 0.773 8.422 16664 Z= 0.415 Chirality : 0.045 0.182 1816 Planarity : 0.007 0.075 2066 Dihedral : 7.938 83.249 1620 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.12 % Favored : 90.45 % Rotamer: Outliers : 3.53 % Allowed : 19.40 % Favored : 77.07 % 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: -4.20 (0.18), residues: 1414 helix: -2.09 (0.15), residues: 798 sheet: -3.75 (0.55), residues: 44 loop : -3.68 (0.21), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 397 HIS 0.003 0.001 HIS A 275 PHE 0.021 0.002 PHE A 385 TYR 0.018 0.002 TYR B 242 ARG 0.008 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 293 time to evaluate : 1.626 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 192 MET cc_start: 0.2762 (tmm) cc_final: 0.2092 (ttp) REVERT: A 395 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: A 415 GLN cc_start: 0.7591 (mp10) cc_final: 0.7318 (mp10) REVERT: A 428 ASN cc_start: 0.8300 (p0) cc_final: 0.8004 (p0) REVERT: A 463 TRP cc_start: 0.6430 (t-100) cc_final: 0.6086 (t-100) REVERT: A 506 GLN cc_start: 0.8735 (mm110) cc_final: 0.8517 (mm110) REVERT: A 542 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.7057 (mmm-85) REVERT: A 558 PHE cc_start: 0.8416 (t80) cc_final: 0.8119 (t80) REVERT: A 616 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8247 (tptp) REVERT: A 678 VAL cc_start: 0.8962 (m) cc_final: 0.8574 (p) REVERT: A 697 ILE cc_start: 0.9207 (pt) cc_final: 0.8887 (mt) REVERT: A 867 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7945 (mmtp) REVERT: A 870 ARG cc_start: 0.6908 (ttt180) cc_final: 0.6695 (tmt170) REVERT: B 396 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: B 404 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8153 (mm) REVERT: B 415 GLN cc_start: 0.7927 (mp10) cc_final: 0.7642 (mp10) REVERT: B 420 ARG cc_start: 0.6997 (mtt90) cc_final: 0.6659 (mmt90) REVERT: B 463 TRP cc_start: 0.7226 (t-100) cc_final: 0.6862 (t-100) REVERT: B 467 ILE cc_start: 0.8477 (mp) cc_final: 0.8017 (mp) REVERT: B 556 PHE cc_start: 0.8231 (t80) cc_final: 0.7933 (t80) REVERT: B 558 PHE cc_start: 0.7858 (t80) cc_final: 0.7500 (t80) REVERT: B 612 ILE cc_start: 0.8941 (mt) cc_final: 0.8133 (mt) REVERT: B 687 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8811 (mm) REVERT: B 750 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7777 (ptp) REVERT: B 859 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: B 867 LYS cc_start: 0.8663 (mmtm) cc_final: 0.8377 (mmmm) outliers start: 46 outliers final: 28 residues processed: 320 average time/residue: 0.2408 time to fit residues: 110.6566 Evaluate side-chains 282 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 247 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 851 PHE Chi-restraints excluded: chain B residue 859 ASP Chi-restraints excluded: chain B residue 875 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 415 GLN A 621 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12298 Z= 0.197 Angle : 0.736 8.697 16664 Z= 0.388 Chirality : 0.044 0.170 1816 Planarity : 0.006 0.069 2066 Dihedral : 7.072 87.386 1609 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.69 % Favored : 90.03 % Rotamer: Outliers : 3.45 % Allowed : 21.32 % Favored : 75.23 % 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: -3.46 (0.20), residues: 1414 helix: -1.38 (0.17), residues: 804 sheet: -3.27 (0.62), residues: 44 loop : -3.57 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 397 HIS 0.002 0.001 HIS A 275 PHE 0.024 0.002 PHE A 681 TYR 0.014 0.001 TYR B 306 ARG 0.009 0.001 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 284 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5904 (mm) REVERT: A 192 MET cc_start: 0.2572 (tmm) cc_final: 0.1962 (ttp) REVERT: A 395 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7621 (tp30) REVERT: A 415 GLN cc_start: 0.7448 (mp-120) cc_final: 0.7070 (mp10) REVERT: A 428 ASN cc_start: 0.8188 (p0) cc_final: 0.7882 (p0) REVERT: A 558 PHE cc_start: 0.8434 (t80) cc_final: 0.7977 (t80) REVERT: A 678 VAL cc_start: 0.8830 (m) cc_final: 0.8527 (p) REVERT: A 697 ILE cc_start: 0.9190 (pt) cc_final: 0.8853 (mt) REVERT: A 867 LYS cc_start: 0.7889 (mmtm) cc_final: 0.7655 (mmtp) REVERT: A 870 ARG cc_start: 0.6902 (ttt180) cc_final: 0.6684 (tmt170) REVERT: B 123 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.5954 (mm) REVERT: B 396 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: B 463 TRP cc_start: 0.7219 (t-100) cc_final: 0.6798 (t-100) REVERT: B 678 VAL cc_start: 0.9034 (m) cc_final: 0.8781 (p) REVERT: B 851 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: B 867 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8400 (mmtm) outliers start: 45 outliers final: 20 residues processed: 314 average time/residue: 0.2190 time to fit residues: 100.9405 Evaluate side-chains 272 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 247 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12298 Z= 0.210 Angle : 0.733 9.788 16664 Z= 0.382 Chirality : 0.044 0.170 1816 Planarity : 0.006 0.061 2066 Dihedral : 6.590 86.708 1599 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.55 % Favored : 90.17 % Rotamer: Outliers : 3.76 % Allowed : 23.08 % Favored : 73.16 % 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 (0.21), residues: 1414 helix: -0.91 (0.17), residues: 794 sheet: -2.80 (0.71), residues: 44 loop : -3.47 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 397 HIS 0.002 0.001 HIS A 143 PHE 0.047 0.002 PHE A 485 TYR 0.020 0.001 TYR B 580 ARG 0.007 0.001 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 271 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5910 (mm) REVERT: A 133 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: A 192 MET cc_start: 0.2748 (tmm) cc_final: 0.2134 (ttp) REVERT: A 403 GLU cc_start: 0.7791 (pt0) cc_final: 0.6833 (pt0) REVERT: A 415 GLN cc_start: 0.7519 (mp-120) cc_final: 0.7178 (mp10) REVERT: A 428 ASN cc_start: 0.8224 (p0) cc_final: 0.7889 (p0) REVERT: A 535 ILE cc_start: 0.9092 (tp) cc_final: 0.8587 (tp) REVERT: A 558 PHE cc_start: 0.8448 (t80) cc_final: 0.7949 (t80) REVERT: A 678 VAL cc_start: 0.8888 (m) cc_final: 0.8645 (p) REVERT: A 685 PHE cc_start: 0.8180 (t80) cc_final: 0.7914 (t80) REVERT: A 697 ILE cc_start: 0.9166 (pt) cc_final: 0.8883 (mt) REVERT: A 870 ARG cc_start: 0.6911 (ttt180) cc_final: 0.6707 (tmt170) REVERT: B 123 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6190 (mm) REVERT: B 294 GLU cc_start: 0.8173 (tp30) cc_final: 0.7890 (tp30) REVERT: B 323 TYR cc_start: 0.7756 (t80) cc_final: 0.7226 (t80) REVERT: B 396 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: B 415 GLN cc_start: 0.7952 (mp10) cc_final: 0.7466 (mp10) REVERT: B 463 TRP cc_start: 0.7197 (t-100) cc_final: 0.6817 (t-100) REVERT: B 468 ILE cc_start: 0.9120 (tt) cc_final: 0.8876 (mt) REVERT: B 678 VAL cc_start: 0.9027 (m) cc_final: 0.8737 (p) REVERT: B 851 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: B 867 LYS cc_start: 0.8319 (mmtm) cc_final: 0.7936 (mmmt) outliers start: 49 outliers final: 27 residues processed: 303 average time/residue: 0.1977 time to fit residues: 90.1264 Evaluate side-chains 279 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 247 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12298 Z= 0.285 Angle : 0.759 10.195 16664 Z= 0.399 Chirality : 0.046 0.220 1816 Planarity : 0.006 0.054 2066 Dihedral : 6.053 37.720 1594 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.33 % Favored : 89.39 % Rotamer: Outliers : 4.37 % Allowed : 23.47 % Favored : 72.16 % 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: -2.83 (0.21), residues: 1414 helix: -0.72 (0.18), residues: 808 sheet: -2.89 (0.70), residues: 44 loop : -3.58 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 397 HIS 0.004 0.001 HIS A 143 PHE 0.025 0.002 PHE A 485 TYR 0.017 0.002 TYR A 255 ARG 0.009 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 253 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: A 192 MET cc_start: 0.2416 (tmm) cc_final: 0.1815 (ttp) REVERT: A 309 MET cc_start: 0.8188 (mmp) cc_final: 0.7836 (tpp) REVERT: A 348 MET cc_start: 0.7671 (ptp) cc_final: 0.7455 (ptt) REVERT: A 403 GLU cc_start: 0.7838 (pt0) cc_final: 0.7288 (pt0) REVERT: A 415 GLN cc_start: 0.7705 (mp-120) cc_final: 0.7199 (mp10) REVERT: A 428 ASN cc_start: 0.8245 (p0) cc_final: 0.7927 (p0) REVERT: A 558 PHE cc_start: 0.8455 (t80) cc_final: 0.8036 (t80) REVERT: A 678 VAL cc_start: 0.8962 (m) cc_final: 0.8680 (p) REVERT: A 685 PHE cc_start: 0.8237 (t80) cc_final: 0.7801 (t80) REVERT: A 697 ILE cc_start: 0.9210 (pt) cc_final: 0.8984 (mt) REVERT: B 123 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6378 (mm) REVERT: B 323 TYR cc_start: 0.7846 (t80) cc_final: 0.7338 (t80) REVERT: B 396 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: B 415 GLN cc_start: 0.8147 (mp10) cc_final: 0.7472 (pm20) REVERT: B 463 TRP cc_start: 0.7305 (t-100) cc_final: 0.6932 (t-100) REVERT: B 678 VAL cc_start: 0.9096 (m) cc_final: 0.8869 (p) REVERT: B 851 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7867 (m-80) outliers start: 57 outliers final: 39 residues processed: 288 average time/residue: 0.2143 time to fit residues: 93.2436 Evaluate side-chains 277 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 234 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 706 LYS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 34 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12298 Z= 0.187 Angle : 0.750 12.319 16664 Z= 0.384 Chirality : 0.044 0.180 1816 Planarity : 0.005 0.051 2066 Dihedral : 5.892 33.739 1594 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.05 % Favored : 90.66 % Rotamer: Outliers : 3.45 % Allowed : 26.00 % Favored : 70.55 % 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: -2.56 (0.21), residues: 1414 helix: -0.52 (0.18), residues: 804 sheet: -2.48 (0.70), residues: 44 loop : -3.43 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 397 HIS 0.002 0.000 HIS B 143 PHE 0.049 0.002 PHE A 485 TYR 0.023 0.001 TYR A 242 ARG 0.006 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 270 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: A 192 MET cc_start: 0.2698 (tmm) cc_final: 0.2062 (ttp) REVERT: A 415 GLN cc_start: 0.7586 (mp-120) cc_final: 0.7104 (mp10) REVERT: A 428 ASN cc_start: 0.8280 (p0) cc_final: 0.7950 (p0) REVERT: A 558 PHE cc_start: 0.8407 (t80) cc_final: 0.7963 (t80) REVERT: A 678 VAL cc_start: 0.8956 (m) cc_final: 0.8698 (p) REVERT: A 685 PHE cc_start: 0.8217 (t80) cc_final: 0.7790 (t80) REVERT: A 697 ILE cc_start: 0.9140 (pt) cc_final: 0.8855 (mm) REVERT: A 773 MET cc_start: 0.8390 (mpp) cc_final: 0.8178 (mpp) REVERT: A 851 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: B 123 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6240 (mm) REVERT: B 396 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: B 415 GLN cc_start: 0.8262 (mp10) cc_final: 0.7834 (mp10) REVERT: B 463 TRP cc_start: 0.7230 (t-100) cc_final: 0.6878 (t-100) REVERT: B 616 LYS cc_start: 0.9204 (tptt) cc_final: 0.8979 (tptp) REVERT: B 678 VAL cc_start: 0.9145 (m) cc_final: 0.8892 (p) REVERT: B 851 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7878 (m-80) outliers start: 45 outliers final: 27 residues processed: 297 average time/residue: 0.2024 time to fit residues: 90.0740 Evaluate side-chains 282 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 250 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12298 Z= 0.249 Angle : 0.770 10.104 16664 Z= 0.397 Chirality : 0.045 0.213 1816 Planarity : 0.005 0.051 2066 Dihedral : 5.870 34.571 1594 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.04 % Favored : 89.67 % Rotamer: Outliers : 3.91 % Allowed : 27.61 % Favored : 68.48 % 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: -2.31 (0.22), residues: 1414 helix: -0.26 (0.18), residues: 800 sheet: -2.42 (0.69), residues: 44 loop : -3.42 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 359 HIS 0.003 0.001 HIS A 129 PHE 0.027 0.002 PHE A 485 TYR 0.015 0.001 TYR A 242 ARG 0.006 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 253 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: A 123 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5925 (mm) REVERT: A 133 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7443 (tp30) REVERT: A 192 MET cc_start: 0.2605 (tmm) cc_final: 0.2027 (ttp) REVERT: A 415 GLN cc_start: 0.7627 (mp-120) cc_final: 0.7152 (mp10) REVERT: A 428 ASN cc_start: 0.8311 (p0) cc_final: 0.7967 (p0) REVERT: A 463 TRP cc_start: 0.7481 (t-100) cc_final: 0.7263 (t-100) REVERT: A 539 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: A 558 PHE cc_start: 0.8440 (t80) cc_final: 0.7834 (t80) REVERT: A 678 VAL cc_start: 0.8993 (m) cc_final: 0.8697 (p) REVERT: A 685 PHE cc_start: 0.8433 (t80) cc_final: 0.7862 (t80) REVERT: A 697 ILE cc_start: 0.9191 (pt) cc_final: 0.8908 (mm) REVERT: A 851 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: B 123 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6490 (mm) REVERT: B 396 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: B 415 GLN cc_start: 0.8336 (mp10) cc_final: 0.7933 (mp10) REVERT: B 463 TRP cc_start: 0.7251 (t-100) cc_final: 0.6908 (t-100) REVERT: B 678 VAL cc_start: 0.9157 (m) cc_final: 0.8939 (p) REVERT: B 851 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7881 (m-80) outliers start: 51 outliers final: 32 residues processed: 285 average time/residue: 0.1970 time to fit residues: 84.9779 Evaluate side-chains 281 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 765 TYR Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 chunk 88 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12298 Z= 0.199 Angle : 0.783 14.857 16664 Z= 0.394 Chirality : 0.044 0.186 1816 Planarity : 0.005 0.052 2066 Dihedral : 5.764 32.971 1594 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.12 % Favored : 90.59 % Rotamer: Outliers : 3.45 % Allowed : 27.76 % Favored : 68.79 % 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: -2.27 (0.22), residues: 1414 helix: -0.26 (0.18), residues: 804 sheet: -2.01 (0.71), residues: 44 loop : -3.39 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 359 HIS 0.002 0.000 HIS A 830 PHE 0.050 0.002 PHE A 485 TYR 0.012 0.001 TYR B 323 ARG 0.011 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 269 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: A 192 MET cc_start: 0.3029 (tmm) cc_final: 0.2459 (ttp) REVERT: A 415 GLN cc_start: 0.7581 (mp-120) cc_final: 0.7169 (mp10) REVERT: A 428 ASN cc_start: 0.8330 (p0) cc_final: 0.8001 (p0) REVERT: A 558 PHE cc_start: 0.8423 (t80) cc_final: 0.7979 (t80) REVERT: A 678 VAL cc_start: 0.8939 (m) cc_final: 0.8636 (p) REVERT: A 685 PHE cc_start: 0.8325 (t80) cc_final: 0.7776 (t80) REVERT: A 697 ILE cc_start: 0.9140 (pt) cc_final: 0.8935 (mm) REVERT: A 851 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: B 123 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6485 (mm) REVERT: B 133 GLU cc_start: 0.7837 (tp30) cc_final: 0.7272 (tp30) REVERT: B 396 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: B 415 GLN cc_start: 0.8321 (mp10) cc_final: 0.7860 (mp10) REVERT: B 463 TRP cc_start: 0.7198 (t-100) cc_final: 0.6860 (t-100) REVERT: B 468 ILE cc_start: 0.9110 (mt) cc_final: 0.8831 (mt) REVERT: B 616 LYS cc_start: 0.9183 (tptt) cc_final: 0.8924 (tptp) REVERT: B 678 VAL cc_start: 0.9085 (m) cc_final: 0.8861 (p) REVERT: B 697 ILE cc_start: 0.9314 (pt) cc_final: 0.8930 (mm) REVERT: B 851 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7895 (m-80) outliers start: 45 outliers final: 30 residues processed: 293 average time/residue: 0.1996 time to fit residues: 87.8640 Evaluate side-chains 289 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 254 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12298 Z= 0.205 Angle : 0.788 15.124 16664 Z= 0.397 Chirality : 0.046 0.419 1816 Planarity : 0.005 0.051 2066 Dihedral : 5.682 33.546 1594 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.48 % Favored : 90.24 % Rotamer: Outliers : 3.22 % Allowed : 28.30 % Favored : 68.48 % 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: -2.15 (0.22), residues: 1414 helix: -0.14 (0.18), residues: 802 sheet: -1.82 (0.73), residues: 44 loop : -3.37 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 273 HIS 0.002 0.000 HIS A 129 PHE 0.053 0.002 PHE A 485 TYR 0.012 0.001 TYR A 323 ARG 0.006 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 255 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: A 192 MET cc_start: 0.2901 (tmm) cc_final: 0.2259 (ttp) REVERT: A 428 ASN cc_start: 0.8339 (p0) cc_final: 0.8023 (p0) REVERT: A 558 PHE cc_start: 0.8455 (t80) cc_final: 0.7945 (t80) REVERT: A 685 PHE cc_start: 0.8381 (t80) cc_final: 0.7788 (t80) REVERT: B 123 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6592 (mm) REVERT: B 133 GLU cc_start: 0.7805 (tp30) cc_final: 0.7257 (tp30) REVERT: B 295 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7943 (mtmm) REVERT: B 332 THR cc_start: 0.7850 (p) cc_final: 0.7612 (t) REVERT: B 396 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: B 415 GLN cc_start: 0.8295 (mp10) cc_final: 0.7821 (mp10) REVERT: B 463 TRP cc_start: 0.7194 (t-100) cc_final: 0.6864 (t-100) REVERT: B 468 ILE cc_start: 0.9098 (mt) cc_final: 0.8796 (mt) REVERT: B 678 VAL cc_start: 0.9104 (m) cc_final: 0.8897 (p) REVERT: B 697 ILE cc_start: 0.9339 (pt) cc_final: 0.8944 (mm) REVERT: B 851 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7874 (m-80) outliers start: 42 outliers final: 32 residues processed: 281 average time/residue: 0.1926 time to fit residues: 82.8653 Evaluate side-chains 275 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 239 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 90 optimal weight: 0.2980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS B 330 ASN B 674 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12298 Z= 0.228 Angle : 0.814 15.286 16664 Z= 0.412 Chirality : 0.047 0.345 1816 Planarity : 0.005 0.052 2066 Dihedral : 5.689 35.057 1594 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.69 % Favored : 90.03 % Rotamer: Outliers : 3.37 % Allowed : 28.76 % Favored : 67.87 % 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: -2.10 (0.22), residues: 1414 helix: -0.11 (0.18), residues: 802 sheet: -1.73 (0.74), residues: 44 loop : -3.35 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 273 HIS 0.002 0.001 HIS A 129 PHE 0.050 0.002 PHE B 485 TYR 0.011 0.001 TYR B 406 ARG 0.006 0.000 ARG A 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 242 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: A 192 MET cc_start: 0.2749 (tmm) cc_final: 0.2153 (ttp) REVERT: A 428 ASN cc_start: 0.8355 (p0) cc_final: 0.8029 (p0) REVERT: A 468 ILE cc_start: 0.9221 (tt) cc_final: 0.8951 (mt) REVERT: A 558 PHE cc_start: 0.8450 (t80) cc_final: 0.8002 (t80) REVERT: A 685 PHE cc_start: 0.8427 (t80) cc_final: 0.7886 (t80) REVERT: B 123 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6595 (mm) REVERT: B 133 GLU cc_start: 0.7797 (tp30) cc_final: 0.7255 (tp30) REVERT: B 295 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7820 (mtmm) REVERT: B 332 THR cc_start: 0.7916 (p) cc_final: 0.7698 (t) REVERT: B 364 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7828 (m) REVERT: B 396 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: B 415 GLN cc_start: 0.8302 (mp10) cc_final: 0.7822 (mp10) REVERT: B 463 TRP cc_start: 0.7213 (t-100) cc_final: 0.6891 (t-100) REVERT: B 697 ILE cc_start: 0.9355 (pt) cc_final: 0.8959 (mm) REVERT: B 750 MET cc_start: 0.7835 (ppp) cc_final: 0.7487 (ptm) REVERT: B 851 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: B 867 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7941 (mmmt) outliers start: 44 outliers final: 32 residues processed: 269 average time/residue: 0.1942 time to fit residues: 79.2920 Evaluate side-chains 273 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN B 674 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.103832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.087793 restraints weight = 37564.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089387 restraints weight = 24577.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.090408 restraints weight = 18409.157| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12298 Z= 0.220 Angle : 0.814 15.120 16664 Z= 0.410 Chirality : 0.047 0.363 1816 Planarity : 0.005 0.052 2066 Dihedral : 5.690 35.873 1594 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.83 % Favored : 89.89 % Rotamer: Outliers : 3.22 % Allowed : 29.06 % Favored : 67.71 % 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: -2.03 (0.22), residues: 1414 helix: -0.05 (0.18), residues: 802 sheet: -1.65 (0.76), residues: 44 loop : -3.33 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 273 HIS 0.002 0.000 HIS A 129 PHE 0.027 0.002 PHE A 851 TYR 0.012 0.001 TYR A 323 ARG 0.005 0.000 ARG A 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.59 seconds wall clock time: 46 minutes 43.98 seconds (2803.98 seconds total)