Starting phenix.real_space_refine on Sun Feb 18 13:38:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2024/6bwf_7298.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2024/6bwf_7298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2024/6bwf_7298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2024/6bwf_7298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2024/6bwf_7298.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2024/6bwf_7298.pdb" } resolution = 4.1 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= 0.004 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 116 5.16 5 C 14320 2.51 5 N 3789 2.21 5 O 3949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "B ARG 288": "NH1" <-> "NH2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 383": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "B ARG 596": "NH1" <-> "NH2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B ARG 769": "NH1" <-> "NH2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 383": "NH1" <-> "NH2" Residue "C ARG 497": "NH1" <-> "NH2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "C ARG 596": "NH1" <-> "NH2" Residue "C ARG 616": "NH1" <-> "NH2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C ARG 769": "NH1" <-> "NH2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "D ARG 383": "NH1" <-> "NH2" Residue "D ARG 497": "NH1" <-> "NH2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "D ARG 596": "NH1" <-> "NH2" Residue "D ARG 616": "NH1" <-> "NH2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D ARG 769": "NH1" <-> "NH2" Residue "D ARG 852": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22174 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5546 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 234} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 685 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 337 Chain: "B" Number of atoms: 5532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5532 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 237} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 700 Unresolved non-hydrogen angles: 946 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 7, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 348 Chain: "C" Number of atoms: 5550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5550 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 233} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 681 Unresolved non-hydrogen angles: 922 Unresolved non-hydrogen dihedrals: 493 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 337 Chain: "D" Number of atoms: 5546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5546 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 234} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 685 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 337 Time building chain proxies: 11.21, per 1000 atoms: 0.51 Number of scatterers: 22174 At special positions: 0 Unit cell: (135.3, 135.3, 153.75, 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 116 16.00 O 3949 8.00 N 3789 7.00 C 14320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.21 Conformation dependent library (CDL) restraints added in 3.9 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 0 sheets defined 69.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.818A pdb=" N UNK A 35 " --> pdb=" O UNK A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK A 52 " --> pdb=" O UNK A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.516A pdb=" N UNK A 64 " --> pdb=" O UNK A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.689A pdb=" N LEU A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.370A pdb=" N GLN A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 4.395A pdb=" N HIS A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 275 through 286 removed outlier: 4.982A pdb=" N ILE A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 323 removed outlier: 4.745A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 322 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 337 through 354 removed outlier: 4.440A pdb=" N LEU A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 346 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 390 through 397 Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.583A pdb=" N SER A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 429 removed outlier: 4.298A pdb=" N MET A 427 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 428 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU A 429 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 529 removed outlier: 4.394A pdb=" N LEU A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 554 removed outlier: 3.964A pdb=" N VAL A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 574 removed outlier: 4.001A pdb=" N TRP A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 595 removed outlier: 3.525A pdb=" N PHE A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.673A pdb=" N ILE A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.756A pdb=" N ASP A 632 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR A 643 " --> pdb=" O GLN A 639 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY A 648 " --> pdb=" O VAL A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE A 657 " --> pdb=" O ASN A 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 660 " --> pdb=" O TYR A 656 " (cutoff:3.500A) Proline residue: A 671 - end of helix removed outlier: 4.219A pdb=" N ILE A 675 " --> pdb=" O PRO A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.807A pdb=" N ASP A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE A 707 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 738 removed outlier: 3.606A pdb=" N ALA A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 754 through 774 removed outlier: 4.059A pdb=" N ILE A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR A 770 " --> pdb=" O LYS A 766 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS A 771 " --> pdb=" O TYR A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 790 removed outlier: 3.922A pdb=" N LEU A 789 " --> pdb=" O PRO A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 844 removed outlier: 4.426A pdb=" N GLU A 833 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 885 removed outlier: 3.864A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 27 through 35 removed outlier: 3.817A pdb=" N UNK B 35 " --> pdb=" O UNK B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK B 52 " --> pdb=" O UNK B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.515A pdb=" N UNK B 64 " --> pdb=" O UNK B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 123 through 133 removed outlier: 3.689A pdb=" N LEU B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 207 through 212 removed outlier: 4.369A pdb=" N GLN B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 4.395A pdb=" N HIS B 233 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 275 through 286 removed outlier: 4.983A pdb=" N ILE B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 323 removed outlier: 4.746A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 322 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 341 through 354 removed outlier: 4.008A pdb=" N VAL B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 346 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 390 through 397 Processing helix chain 'B' and resid 413 through 421 removed outlier: 3.582A pdb=" N SER B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 429 removed outlier: 4.299A pdb=" N MET B 427 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 428 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU B 429 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 505 through 529 removed outlier: 4.394A pdb=" N LEU B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 554 removed outlier: 3.963A pdb=" N VAL B 543 " --> pdb=" O GLN B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 574 removed outlier: 4.002A pdb=" N TRP B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 595 removed outlier: 3.524A pdb=" N PHE B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 removed outlier: 3.674A pdb=" N ILE B 618 " --> pdb=" O ALA B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 633 removed outlier: 3.755A pdb=" N ASP B 632 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR B 643 " --> pdb=" O GLN B 639 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY B 648 " --> pdb=" O VAL B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE B 657 " --> pdb=" O ASN B 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 660 " --> pdb=" O TYR B 656 " (cutoff:3.500A) Proline residue: B 671 - end of helix removed outlier: 4.219A pdb=" N ILE B 675 " --> pdb=" O PRO B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.806A pdb=" N ASP B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE B 707 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 738 removed outlier: 3.607A pdb=" N ALA B 732 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 754 through 774 removed outlier: 4.059A pdb=" N ILE B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR B 770 " --> pdb=" O LYS B 766 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS B 771 " --> pdb=" O TYR B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 790 removed outlier: 3.923A pdb=" N LEU B 789 " --> pdb=" O PRO B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 844 removed outlier: 4.426A pdb=" N GLU B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP B 841 " --> pdb=" O ASP B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 885 removed outlier: 3.864A pdb=" N ILE B 851 " --> pdb=" O SER B 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 27 through 35 removed outlier: 3.818A pdb=" N UNK C 35 " --> pdb=" O UNK C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK C 52 " --> pdb=" O UNK C 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 49 through 52' Processing helix chain 'C' and resid 55 through 64 removed outlier: 3.515A pdb=" N UNK C 64 " --> pdb=" O UNK C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 Processing helix chain 'C' and resid 123 through 133 removed outlier: 3.690A pdb=" N LEU C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.369A pdb=" N GLN C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 234 removed outlier: 4.394A pdb=" N HIS C 233 " --> pdb=" O ARG C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 275 through 286 removed outlier: 4.982A pdb=" N ILE C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 323 removed outlier: 4.745A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 322 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 335 Processing helix chain 'C' and resid 337 through 354 removed outlier: 5.294A pdb=" N LEU C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 345 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 346 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 390 through 397 Processing helix chain 'C' and resid 413 through 421 removed outlier: 3.582A pdb=" N SER C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 429 removed outlier: 4.299A pdb=" N MET C 427 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 428 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU C 429 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 Processing helix chain 'C' and resid 505 through 529 removed outlier: 4.394A pdb=" N LEU C 518 " --> pdb=" O THR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 554 removed outlier: 3.963A pdb=" N VAL C 543 " --> pdb=" O GLN C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 574 removed outlier: 4.001A pdb=" N TRP C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 595 removed outlier: 3.524A pdb=" N PHE C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 removed outlier: 3.673A pdb=" N ILE C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 633 removed outlier: 3.755A pdb=" N ASP C 632 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR C 643 " --> pdb=" O GLN C 639 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE C 657 " --> pdb=" O ASN C 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE C 660 " --> pdb=" O TYR C 656 " (cutoff:3.500A) Proline residue: C 671 - end of helix removed outlier: 4.219A pdb=" N ILE C 675 " --> pdb=" O PRO C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.807A pdb=" N ASP C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N HIS C 693 " --> pdb=" O ASP C 689 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE C 707 " --> pdb=" O ALA C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 738 removed outlier: 3.607A pdb=" N ALA C 732 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 749 Processing helix chain 'C' and resid 754 through 774 removed outlier: 4.060A pdb=" N ILE C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 763 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR C 770 " --> pdb=" O LYS C 766 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS C 771 " --> pdb=" O TYR C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 790 removed outlier: 3.923A pdb=" N LEU C 789 " --> pdb=" O PRO C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 844 removed outlier: 4.426A pdb=" N GLU C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 840 " --> pdb=" O PHE C 836 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 885 removed outlier: 3.865A pdb=" N ILE C 851 " --> pdb=" O SER C 847 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 27 through 35 removed outlier: 3.818A pdb=" N UNK D 35 " --> pdb=" O UNK D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 48 Processing helix chain 'D' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK D 52 " --> pdb=" O UNK D 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 55 through 64 removed outlier: 3.515A pdb=" N UNK D 64 " --> pdb=" O UNK D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 123 through 133 removed outlier: 3.690A pdb=" N LEU D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 171 through 176 Processing helix chain 'D' and resid 207 through 212 removed outlier: 4.369A pdb=" N GLN D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 234 removed outlier: 4.395A pdb=" N HIS D 233 " --> pdb=" O ARG D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 275 through 286 removed outlier: 4.983A pdb=" N ILE D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 323 removed outlier: 4.745A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 322 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 337 through 354 removed outlier: 5.295A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL D 345 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 346 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 354 " --> pdb=" O GLN D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 390 through 397 Processing helix chain 'D' and resid 413 through 421 removed outlier: 3.583A pdb=" N SER D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 420 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 429 removed outlier: 4.299A pdb=" N MET D 427 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 428 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU D 429 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 505 through 529 removed outlier: 4.393A pdb=" N LEU D 518 " --> pdb=" O THR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 554 removed outlier: 3.963A pdb=" N VAL D 543 " --> pdb=" O GLN D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 574 removed outlier: 4.001A pdb=" N TRP D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 595 removed outlier: 3.524A pdb=" N PHE D 593 " --> pdb=" O PHE D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 622 removed outlier: 3.673A pdb=" N ILE D 618 " --> pdb=" O ALA D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 633 removed outlier: 3.756A pdb=" N ASP D 632 " --> pdb=" O VAL D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR D 643 " --> pdb=" O GLN D 639 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE D 657 " --> pdb=" O ASN D 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE D 660 " --> pdb=" O TYR D 656 " (cutoff:3.500A) Proline residue: D 671 - end of helix removed outlier: 4.219A pdb=" N ILE D 675 " --> pdb=" O PRO D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.807A pdb=" N ASP D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS D 693 " --> pdb=" O ASP D 689 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE D 707 " --> pdb=" O ALA D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 738 removed outlier: 3.606A pdb=" N ALA D 732 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 736 " --> pdb=" O ALA D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 749 Processing helix chain 'D' and resid 754 through 774 removed outlier: 4.059A pdb=" N ILE D 760 " --> pdb=" O GLN D 756 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE D 763 " --> pdb=" O ALA D 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR D 770 " --> pdb=" O LYS D 766 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS D 771 " --> pdb=" O TYR D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 790 removed outlier: 3.922A pdb=" N LEU D 789 " --> pdb=" O PRO D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 844 removed outlier: 4.425A pdb=" N GLU D 833 " --> pdb=" O GLU D 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP D 841 " --> pdb=" O ASP D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 885 removed outlier: 3.865A pdb=" N ILE D 851 " --> pdb=" O SER D 847 " (cutoff:3.500A) 974 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 9.81 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: 6355 1.34 - 1.45: 4381 1.45 - 1.57: 11665 1.57 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 22601 Sorted by residual: bond pdb=" C ARG C 242 " pdb=" N PRO C 243 " ideal model delta sigma weight residual 1.332 1.378 -0.046 8.90e-03 1.26e+04 2.66e+01 bond pdb=" C ARG B 242 " pdb=" N PRO B 243 " ideal model delta sigma weight residual 1.332 1.378 -0.045 8.90e-03 1.26e+04 2.61e+01 bond pdb=" C ARG D 242 " pdb=" N PRO D 243 " ideal model delta sigma weight residual 1.332 1.378 -0.045 8.90e-03 1.26e+04 2.60e+01 bond pdb=" C ARG A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.332 1.377 -0.044 8.90e-03 1.26e+04 2.50e+01 bond pdb=" C GLN A 239 " pdb=" N PRO A 240 " ideal model delta sigma weight residual 1.337 1.376 -0.040 1.11e-02 8.12e+03 1.29e+01 ... (remaining 22596 not shown) Histogram of bond angle deviations from ideal: 96.92 - 104.71: 334 104.71 - 112.50: 11049 112.50 - 120.29: 10239 120.29 - 128.08: 8779 128.08 - 135.86: 295 Bond angle restraints: 30696 Sorted by residual: angle pdb=" N HIS A 777 " pdb=" CA HIS A 777 " pdb=" C HIS A 777 " ideal model delta sigma weight residual 110.80 127.91 -17.11 2.13e+00 2.20e-01 6.46e+01 angle pdb=" N HIS B 777 " pdb=" CA HIS B 777 " pdb=" C HIS B 777 " ideal model delta sigma weight residual 110.80 127.90 -17.10 2.13e+00 2.20e-01 6.44e+01 angle pdb=" N HIS D 777 " pdb=" CA HIS D 777 " pdb=" C HIS D 777 " ideal model delta sigma weight residual 110.80 127.87 -17.07 2.13e+00 2.20e-01 6.43e+01 angle pdb=" N HIS C 777 " pdb=" CA HIS C 777 " pdb=" C HIS C 777 " ideal model delta sigma weight residual 110.80 127.86 -17.06 2.13e+00 2.20e-01 6.41e+01 angle pdb=" C TRP B 601 " pdb=" N ASN B 602 " pdb=" CA ASN B 602 " ideal model delta sigma weight residual 121.70 135.86 -14.16 1.80e+00 3.09e-01 6.19e+01 ... (remaining 30691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 12933 26.67 - 53.34: 319 53.34 - 80.00: 24 80.00 - 106.67: 0 106.67 - 133.34: 8 Dihedral angle restraints: 13284 sinusoidal: 4269 harmonic: 9015 Sorted by residual: dihedral pdb=" CA TYR C 776 " pdb=" C TYR C 776 " pdb=" N HIS C 777 " pdb=" CA HIS C 777 " ideal model delta harmonic sigma weight residual -180.00 -46.66 -133.34 0 5.00e+00 4.00e-02 7.11e+02 dihedral pdb=" CA TYR B 776 " pdb=" C TYR B 776 " pdb=" N HIS B 777 " pdb=" CA HIS B 777 " ideal model delta harmonic sigma weight residual -180.00 -46.68 -133.32 0 5.00e+00 4.00e-02 7.11e+02 dihedral pdb=" CA TYR A 776 " pdb=" C TYR A 776 " pdb=" N HIS A 777 " pdb=" CA HIS A 777 " ideal model delta harmonic sigma weight residual -180.00 -46.69 -133.31 0 5.00e+00 4.00e-02 7.11e+02 ... (remaining 13281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3077 0.093 - 0.186: 380 0.186 - 0.279: 58 0.279 - 0.372: 9 0.372 - 0.465: 7 Chirality restraints: 3531 Sorted by residual: chirality pdb=" CA HIS D 777 " pdb=" N HIS D 777 " pdb=" C HIS D 777 " pdb=" CB HIS D 777 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA HIS B 777 " pdb=" N HIS B 777 " pdb=" C HIS B 777 " pdb=" CB HIS B 777 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA HIS C 777 " pdb=" N HIS C 777 " pdb=" C HIS C 777 " pdb=" CB HIS C 777 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 3528 not shown) Planarity restraints: 3910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 512 " -0.033 2.00e-02 2.50e+03 3.18e-02 1.76e+01 pdb=" CG PHE D 512 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE D 512 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE D 512 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 512 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 512 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE D 512 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 512 " 0.033 2.00e-02 2.50e+03 3.18e-02 1.76e+01 pdb=" CG PHE C 512 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE C 512 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 512 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 512 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 512 " 0.023 2.00e-02 2.50e+03 pdb=" CZ PHE C 512 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 512 " -0.033 2.00e-02 2.50e+03 3.17e-02 1.75e+01 pdb=" CG PHE A 512 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 512 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 512 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 512 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 512 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 512 " 0.005 2.00e-02 2.50e+03 ... (remaining 3907 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5649 2.79 - 3.32: 21152 3.32 - 3.85: 34490 3.85 - 4.37: 38935 4.37 - 4.90: 62040 Nonbonded interactions: 162266 Sorted by model distance: nonbonded pdb=" O SER B 337 " pdb=" N ASP B 339 " model vdw 2.263 2.520 nonbonded pdb=" O PHE B 578 " pdb=" OG SER B 581 " model vdw 2.272 2.440 nonbonded pdb=" O PHE C 578 " pdb=" OG SER C 581 " model vdw 2.272 2.440 nonbonded pdb=" O PHE A 578 " pdb=" OG SER A 581 " model vdw 2.273 2.440 nonbonded pdb=" O PHE D 578 " pdb=" OG SER D 581 " model vdw 2.273 2.440 ... (remaining 162261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 331 or (resid 332 through 334 and (name N or nam \ e CA or name C or name O or name CB )) or resid 335 or (resid 336 and (name N or \ name CA or name C or name O or name CB )) or resid 337 through 886)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 331 or (resid 332 through 334 and (name N or nam \ e CA or name C or name O or name CB )) or resid 335 or (resid 336 and (name N or \ name CA or name C or name O or name CB )) or resid 337 through 886)) selection = (chain 'D' and (resid 1 through 331 or (resid 332 through 334 and (name N or nam \ e CA or name C or name O or name CB )) or resid 335 or (resid 336 and (name N or \ name CA or name C or name O or name CB )) or resid 337 through 886)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.750 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 54.450 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.090 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 22601 Z= 0.481 Angle : 1.514 17.114 30696 Z= 0.885 Chirality : 0.070 0.465 3531 Planarity : 0.008 0.076 3910 Dihedral : 12.820 133.338 7388 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 1.32 % Allowed : 12.10 % Favored : 86.58 % Rotamer: Outliers : 0.59 % Allowed : 5.20 % Favored : 94.21 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 4.93 % Twisted Proline : 11.11 % Twisted General : 2.80 % 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: -5.34 (0.14), residues: 2496 helix: -3.42 (0.10), residues: 1504 sheet: None (None), residues: 0 loop : -3.57 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 282 HIS 0.007 0.002 HIS B 693 PHE 0.071 0.004 PHE D 512 TYR 0.026 0.003 TYR A 643 ARG 0.009 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 803 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.9276 (mt) cc_final: 0.8964 (tp) REVERT: A 213 ARG cc_start: 0.7587 (mtt180) cc_final: 0.6836 (mtt180) REVERT: A 303 MET cc_start: 0.8458 (tmt) cc_final: 0.8037 (tmm) REVERT: A 634 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7350 (tt) REVERT: A 665 LEU cc_start: 0.8051 (tm) cc_final: 0.7806 (tp) REVERT: A 825 HIS cc_start: 0.6449 (m-70) cc_final: 0.6091 (m-70) REVERT: B 159 TYR cc_start: 0.5768 (p90) cc_final: 0.5561 (p90) REVERT: B 249 MET cc_start: 0.7770 (ptp) cc_final: 0.6894 (ptp) REVERT: B 251 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7429 (mm-30) REVERT: B 289 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6929 (tp40) REVERT: B 301 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6191 (mt-10) REVERT: B 509 LYS cc_start: 0.8852 (mttt) cc_final: 0.8302 (tttp) REVERT: B 548 PHE cc_start: 0.7378 (t80) cc_final: 0.7102 (t80) REVERT: B 583 THR cc_start: 0.8360 (p) cc_final: 0.8137 (p) REVERT: B 634 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6769 (tt) REVERT: B 651 VAL cc_start: 0.9114 (t) cc_final: 0.8871 (t) REVERT: B 661 MET cc_start: 0.6828 (mmp) cc_final: 0.6147 (tpp) REVERT: B 673 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8783 (mttp) REVERT: C 169 VAL cc_start: 0.7162 (t) cc_final: 0.6667 (t) REVERT: C 249 MET cc_start: 0.7843 (ptp) cc_final: 0.7559 (ptp) REVERT: C 313 TYR cc_start: 0.8109 (m-10) cc_final: 0.7022 (m-10) REVERT: C 349 GLU cc_start: 0.8191 (tt0) cc_final: 0.7867 (tt0) REVERT: C 634 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7941 (tm) REVERT: C 649 LYS cc_start: 0.8320 (ttmp) cc_final: 0.6802 (tptt) REVERT: C 684 TRP cc_start: 0.6678 (p-90) cc_final: 0.3985 (m-10) REVERT: C 756 GLN cc_start: 0.8643 (pt0) cc_final: 0.8080 (pp30) REVERT: C 830 GLN cc_start: 0.8542 (tt0) cc_final: 0.8118 (tm-30) REVERT: C 859 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6058 (tp30) REVERT: D 213 ARG cc_start: 0.7530 (mtt180) cc_final: 0.6821 (mtt180) REVERT: D 289 GLN cc_start: 0.6188 (mm-40) cc_final: 0.5781 (mm-40) REVERT: D 297 GLN cc_start: 0.7943 (tp40) cc_final: 0.7358 (tp40) REVERT: D 303 MET cc_start: 0.8475 (tmt) cc_final: 0.7789 (tmm) REVERT: D 634 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7779 (tp) REVERT: D 825 HIS cc_start: 0.6423 (m-70) cc_final: 0.6068 (m-70) REVERT: D 859 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6523 (tp30) outliers start: 11 outliers final: 0 residues processed: 814 average time/residue: 0.3248 time to fit residues: 408.8085 Evaluate side-chains 523 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 519 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.9990 chunk 230 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 92 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 0.3980 chunk 276 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A 406 ASN A 504 HIS ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 HIS B 821 GLN B 873 ASN C 390 HIS ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 568 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN D 504 HIS ** D 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 HIS D 864 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22601 Z= 0.264 Angle : 0.925 12.421 30696 Z= 0.490 Chirality : 0.047 0.310 3531 Planarity : 0.005 0.067 3910 Dihedral : 8.470 57.984 3211 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.26 % Favored : 89.26 % Rotamer: Outliers : 0.54 % Allowed : 3.43 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.72 % Twisted Proline : 11.11 % Twisted General : 1.19 % 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: -3.52 (0.16), residues: 2496 helix: -1.63 (0.12), residues: 1580 sheet: None (None), residues: 0 loop : -3.53 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 765 HIS 0.012 0.001 HIS C 825 PHE 0.040 0.003 PHE C 815 TYR 0.025 0.002 TYR A 336 ARG 0.008 0.001 ARG D 871 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 630 time to evaluate : 2.373 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: A 213 ARG cc_start: 0.7457 (mtt180) cc_final: 0.6436 (mmm160) REVERT: A 249 MET cc_start: 0.7752 (ptp) cc_final: 0.7345 (pmm) REVERT: A 394 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8133 (tp40) REVERT: A 509 LYS cc_start: 0.8701 (mttt) cc_final: 0.8367 (tttp) REVERT: A 532 MET cc_start: 0.7802 (tpp) cc_final: 0.7267 (tpp) REVERT: A 558 VAL cc_start: 0.7158 (m) cc_final: 0.6791 (m) REVERT: A 622 ASN cc_start: 0.7805 (t0) cc_final: 0.7458 (t0) REVERT: A 661 MET cc_start: 0.7675 (mmp) cc_final: 0.6368 (mmm) REVERT: A 673 LYS cc_start: 0.9091 (mtpp) cc_final: 0.8725 (mtpp) REVERT: A 689 ASP cc_start: 0.8169 (t0) cc_final: 0.7610 (t0) REVERT: A 713 ASP cc_start: 0.7299 (m-30) cc_final: 0.7040 (t70) REVERT: A 825 HIS cc_start: 0.6564 (m-70) cc_final: 0.6242 (m-70) REVERT: B 125 ILE cc_start: 0.8984 (mm) cc_final: 0.8350 (mm) REVERT: B 159 TYR cc_start: 0.6191 (p90) cc_final: 0.5783 (p90) REVERT: B 213 ARG cc_start: 0.7323 (mtt180) cc_final: 0.6177 (mmm160) REVERT: B 305 LYS cc_start: 0.8884 (ttmt) cc_final: 0.8678 (ttmt) REVERT: B 349 GLU cc_start: 0.7380 (pt0) cc_final: 0.7152 (pt0) REVERT: B 509 LYS cc_start: 0.8655 (mttt) cc_final: 0.8449 (tttp) REVERT: B 558 VAL cc_start: 0.6927 (m) cc_final: 0.6689 (m) REVERT: B 654 MET cc_start: 0.7139 (ptm) cc_final: 0.6672 (ptm) REVERT: B 697 MET cc_start: 0.8721 (mmm) cc_final: 0.8278 (mmm) REVERT: B 713 ASP cc_start: 0.6889 (m-30) cc_final: 0.6631 (t70) REVERT: B 761 SER cc_start: 0.9102 (p) cc_final: 0.8300 (t) REVERT: B 830 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8080 (tm-30) REVERT: B 859 GLU cc_start: 0.7691 (tt0) cc_final: 0.7460 (tm-30) REVERT: C 313 TYR cc_start: 0.8580 (m-10) cc_final: 0.8178 (m-10) REVERT: C 345 VAL cc_start: 0.9225 (t) cc_final: 0.8948 (t) REVERT: C 361 LYS cc_start: 0.7839 (mttt) cc_final: 0.7638 (mmtp) REVERT: C 540 GLU cc_start: 0.6890 (tt0) cc_final: 0.6554 (tt0) REVERT: C 654 MET cc_start: 0.7535 (ptt) cc_final: 0.7111 (ptt) REVERT: C 673 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8694 (mttp) REVERT: C 713 ASP cc_start: 0.7642 (m-30) cc_final: 0.7278 (t0) REVERT: C 756 GLN cc_start: 0.8710 (pt0) cc_final: 0.8106 (pp30) REVERT: C 772 PHE cc_start: 0.8328 (t80) cc_final: 0.8060 (t80) REVERT: C 830 GLN cc_start: 0.8511 (tt0) cc_final: 0.8200 (tm-30) REVERT: C 866 LYS cc_start: 0.6032 (ttmm) cc_final: 0.5779 (mtmm) REVERT: D 213 ARG cc_start: 0.7468 (mtt180) cc_final: 0.6599 (mmm160) REVERT: D 289 GLN cc_start: 0.6004 (mm-40) cc_final: 0.5692 (mm-40) REVERT: D 314 ARG cc_start: 0.7568 (tpp80) cc_final: 0.7320 (tpp80) REVERT: D 417 LEU cc_start: 0.8236 (tt) cc_final: 0.7758 (tp) REVERT: D 509 LYS cc_start: 0.8567 (mttt) cc_final: 0.8287 (tttp) REVERT: D 622 ASN cc_start: 0.7816 (t0) cc_final: 0.7494 (t0) REVERT: D 661 MET cc_start: 0.7326 (mmp) cc_final: 0.6224 (mmm) REVERT: D 673 LYS cc_start: 0.8872 (mttm) cc_final: 0.8210 (mmtp) REVERT: D 706 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7193 (mm-30) REVERT: D 825 HIS cc_start: 0.6580 (m-70) cc_final: 0.6289 (m-70) REVERT: D 859 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6900 (tp30) outliers start: 10 outliers final: 5 residues processed: 638 average time/residue: 0.3256 time to fit residues: 319.0549 Evaluate side-chains 502 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 497 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 276 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 chunk 246 optimal weight: 0.0170 chunk 274 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 771 HIS B 751 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 GLN C 751 ASN C 864 GLN D 192 ASN ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22601 Z= 0.247 Angle : 0.880 13.327 30696 Z= 0.464 Chirality : 0.046 0.314 3531 Planarity : 0.004 0.058 3910 Dihedral : 7.450 40.715 3211 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.14 % Favored : 89.38 % Rotamer: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.76 % Twisted Proline : 7.41 % Twisted General : 0.82 % 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: -2.78 (0.17), residues: 2496 helix: -0.97 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -3.44 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 370 HIS 0.009 0.001 HIS B 825 PHE 0.049 0.002 PHE D 815 TYR 0.029 0.002 TYR A 627 ARG 0.005 0.000 ARG C 857 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 589 time to evaluate : 2.447 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: A 213 ARG cc_start: 0.7522 (mtt180) cc_final: 0.6849 (mtt180) REVERT: A 509 LYS cc_start: 0.8874 (mttt) cc_final: 0.8579 (tttp) REVERT: A 558 VAL cc_start: 0.7004 (m) cc_final: 0.6764 (m) REVERT: A 622 ASN cc_start: 0.7959 (t0) cc_final: 0.7433 (t0) REVERT: A 673 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8739 (ttmm) REVERT: A 689 ASP cc_start: 0.7954 (t0) cc_final: 0.7711 (t0) REVERT: A 706 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7356 (mm-30) REVERT: A 713 ASP cc_start: 0.7122 (m-30) cc_final: 0.6885 (t0) REVERT: A 738 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8606 (mm-40) REVERT: A 825 HIS cc_start: 0.6497 (m-70) cc_final: 0.6072 (m-70) REVERT: A 830 GLN cc_start: 0.8738 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 125 ILE cc_start: 0.8999 (mm) cc_final: 0.8621 (mm) REVERT: B 159 TYR cc_start: 0.6174 (p90) cc_final: 0.5898 (p90) REVERT: B 303 MET cc_start: 0.8797 (ttt) cc_final: 0.8494 (tpp) REVERT: B 349 GLU cc_start: 0.7436 (pt0) cc_final: 0.7231 (pt0) REVERT: B 622 ASN cc_start: 0.7989 (t0) cc_final: 0.7451 (t0) REVERT: B 654 MET cc_start: 0.7359 (ptm) cc_final: 0.6979 (ptm) REVERT: B 713 ASP cc_start: 0.7196 (m-30) cc_final: 0.6856 (t0) REVERT: B 830 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 859 GLU cc_start: 0.7826 (tt0) cc_final: 0.7606 (tm-30) REVERT: C 349 GLU cc_start: 0.8286 (pt0) cc_final: 0.8036 (tt0) REVERT: C 518 LEU cc_start: 0.8819 (mp) cc_final: 0.8467 (mp) REVERT: C 622 ASN cc_start: 0.7584 (t0) cc_final: 0.7266 (t0) REVERT: C 649 LYS cc_start: 0.8264 (mttm) cc_final: 0.7492 (tptt) REVERT: C 713 ASP cc_start: 0.7886 (m-30) cc_final: 0.7343 (t0) REVERT: C 756 GLN cc_start: 0.8881 (pt0) cc_final: 0.8232 (pp30) REVERT: C 761 SER cc_start: 0.8919 (t) cc_final: 0.8669 (t) REVERT: C 776 TYR cc_start: 0.7458 (p90) cc_final: 0.7174 (p90) REVERT: D 213 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7214 (mtt180) REVERT: D 249 MET cc_start: 0.7715 (ptp) cc_final: 0.7349 (pmm) REVERT: D 420 LEU cc_start: 0.9105 (tp) cc_final: 0.8890 (tp) REVERT: D 622 ASN cc_start: 0.8001 (t0) cc_final: 0.7637 (t0) REVERT: D 673 LYS cc_start: 0.8803 (mttm) cc_final: 0.8530 (mmtp) REVERT: D 706 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7501 (mm-30) REVERT: D 713 ASP cc_start: 0.7309 (t70) cc_final: 0.7089 (t70) REVERT: D 825 HIS cc_start: 0.6694 (m-70) cc_final: 0.6334 (m-70) REVERT: D 857 ARG cc_start: 0.8278 (ttm-80) cc_final: 0.7885 (tpp80) outliers start: 2 outliers final: 2 residues processed: 591 average time/residue: 0.3125 time to fit residues: 288.5286 Evaluate side-chains 490 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 488 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 185 optimal weight: 4.9990 chunk 277 optimal weight: 0.7980 chunk 293 optimal weight: 0.5980 chunk 145 optimal weight: 0.0170 chunk 263 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN B 744 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 HIS ** C 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22601 Z= 0.202 Angle : 0.827 12.001 30696 Z= 0.435 Chirality : 0.045 0.303 3531 Planarity : 0.004 0.053 3910 Dihedral : 6.840 38.183 3211 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.29 % Favored : 90.22 % Rotamer: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.88 % Twisted Proline : 5.56 % Twisted General : 0.49 % 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: -2.26 (0.17), residues: 2496 helix: -0.47 (0.14), residues: 1552 sheet: None (None), residues: 0 loop : -3.29 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 370 HIS 0.008 0.001 HIS B 825 PHE 0.041 0.002 PHE C 512 TYR 0.035 0.001 TYR C 336 ARG 0.012 0.000 ARG C 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 596 time to evaluate : 2.345 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 509 LYS cc_start: 0.8876 (mttt) cc_final: 0.8616 (tttp) REVERT: A 522 MET cc_start: 0.8222 (mtt) cc_final: 0.7809 (mtt) REVERT: A 622 ASN cc_start: 0.8104 (t0) cc_final: 0.7521 (t0) REVERT: A 689 ASP cc_start: 0.7798 (t0) cc_final: 0.7243 (t0) REVERT: A 707 ILE cc_start: 0.8241 (mt) cc_final: 0.7989 (mt) REVERT: A 713 ASP cc_start: 0.7329 (m-30) cc_final: 0.6965 (t0) REVERT: A 724 THR cc_start: 0.9190 (p) cc_final: 0.8862 (t) REVERT: A 825 HIS cc_start: 0.6635 (m-70) cc_final: 0.6221 (m-70) REVERT: A 830 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 864 GLN cc_start: 0.8718 (tt0) cc_final: 0.8435 (tt0) REVERT: B 125 ILE cc_start: 0.8857 (mm) cc_final: 0.8425 (mm) REVERT: B 622 ASN cc_start: 0.7968 (t0) cc_final: 0.7557 (t0) REVERT: B 654 MET cc_start: 0.7135 (ptm) cc_final: 0.6857 (ptm) REVERT: B 673 LYS cc_start: 0.9296 (mtpp) cc_final: 0.9076 (mmtt) REVERT: B 697 MET cc_start: 0.8024 (mmm) cc_final: 0.7756 (mmm) REVERT: B 713 ASP cc_start: 0.7245 (m-30) cc_final: 0.6875 (t0) REVERT: B 830 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 859 GLU cc_start: 0.7801 (tt0) cc_final: 0.7553 (tm-30) REVERT: C 313 TYR cc_start: 0.8569 (m-10) cc_final: 0.8004 (m-10) REVERT: C 509 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7811 (tttt) REVERT: C 649 LYS cc_start: 0.8310 (mttm) cc_final: 0.7549 (tptt) REVERT: C 654 MET cc_start: 0.8001 (ptm) cc_final: 0.7060 (ptm) REVERT: C 713 ASP cc_start: 0.7890 (m-30) cc_final: 0.7328 (t0) REVERT: C 756 GLN cc_start: 0.8786 (pt0) cc_final: 0.8175 (pp30) REVERT: C 763 ILE cc_start: 0.9320 (tp) cc_final: 0.9019 (mt) REVERT: C 776 TYR cc_start: 0.7327 (p90) cc_final: 0.6843 (p90) REVERT: D 213 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7476 (mtt180) REVERT: D 532 MET cc_start: 0.8064 (tpp) cc_final: 0.7328 (tpp) REVERT: D 622 ASN cc_start: 0.7694 (t0) cc_final: 0.7312 (t0) REVERT: D 706 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7502 (mm-30) REVERT: D 713 ASP cc_start: 0.7181 (t70) cc_final: 0.6957 (t70) REVERT: D 776 TYR cc_start: 0.7103 (p90) cc_final: 0.6645 (p90) REVERT: D 857 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.7938 (tpp80) outliers start: 1 outliers final: 0 residues processed: 596 average time/residue: 0.3258 time to fit residues: 304.3611 Evaluate side-chains 493 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 250 optimal weight: 5.9990 chunk 203 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN B 297 GLN B 504 HIS B 731 GLN B 751 ASN ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 777 HIS D 751 ASN D 821 GLN D 825 HIS D 873 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22601 Z= 0.249 Angle : 0.849 11.702 30696 Z= 0.446 Chirality : 0.046 0.309 3531 Planarity : 0.004 0.061 3910 Dihedral : 6.815 37.220 3211 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.82 % Favored : 89.70 % Rotamer: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.88 % Twisted Proline : 2.78 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.17), residues: 2496 helix: -0.32 (0.14), residues: 1568 sheet: None (None), residues: 0 loop : -3.29 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 696 HIS 0.014 0.001 HIS D 825 PHE 0.049 0.002 PHE D 815 TYR 0.030 0.002 TYR A 336 ARG 0.005 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 578 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.7580 (mtt180) cc_final: 0.7318 (mtp180) REVERT: A 400 MET cc_start: 0.8589 (ttm) cc_final: 0.8386 (ttm) REVERT: A 522 MET cc_start: 0.8282 (mtt) cc_final: 0.7845 (mtt) REVERT: A 673 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8576 (mtpp) REVERT: A 713 ASP cc_start: 0.7699 (m-30) cc_final: 0.7058 (t0) REVERT: A 731 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8371 (tm-30) REVERT: A 825 HIS cc_start: 0.6760 (m-70) cc_final: 0.6332 (m-70) REVERT: A 830 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 125 ILE cc_start: 0.8931 (mm) cc_final: 0.8548 (mm) REVERT: B 303 MET cc_start: 0.9013 (ttt) cc_final: 0.8345 (ttm) REVERT: B 654 MET cc_start: 0.7450 (ptm) cc_final: 0.7236 (ptm) REVERT: B 713 ASP cc_start: 0.7493 (m-30) cc_final: 0.6906 (t0) REVERT: B 739 TYR cc_start: 0.7330 (t80) cc_final: 0.6970 (t80) REVERT: B 830 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8192 (tm-30) REVERT: B 852 ARG cc_start: 0.8095 (tmm-80) cc_final: 0.7799 (tmm-80) REVERT: B 859 GLU cc_start: 0.8002 (tt0) cc_final: 0.7645 (tm-30) REVERT: C 207 SER cc_start: 0.8620 (p) cc_final: 0.8171 (t) REVERT: C 313 TYR cc_start: 0.8722 (m-10) cc_final: 0.8418 (m-10) REVERT: C 349 GLU cc_start: 0.8004 (pt0) cc_final: 0.7785 (tt0) REVERT: C 400 MET cc_start: 0.8153 (ttm) cc_final: 0.7901 (ttm) REVERT: C 649 LYS cc_start: 0.8495 (mttm) cc_final: 0.7756 (tptt) REVERT: C 654 MET cc_start: 0.8075 (ptm) cc_final: 0.7344 (ptm) REVERT: C 693 HIS cc_start: 0.8369 (t-90) cc_final: 0.8047 (t-170) REVERT: C 713 ASP cc_start: 0.7949 (m-30) cc_final: 0.7304 (t0) REVERT: C 756 GLN cc_start: 0.8885 (pt0) cc_final: 0.8294 (pp30) REVERT: C 763 ILE cc_start: 0.9275 (tp) cc_final: 0.9027 (mt) REVERT: C 776 TYR cc_start: 0.7450 (p90) cc_final: 0.6793 (p90) REVERT: D 622 ASN cc_start: 0.8032 (t0) cc_final: 0.7502 (t0) REVERT: D 776 TYR cc_start: 0.7221 (p90) cc_final: 0.6445 (p90) outliers start: 1 outliers final: 0 residues processed: 578 average time/residue: 0.3162 time to fit residues: 285.3918 Evaluate side-chains 470 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 470 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.5980 chunk 264 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 289 GLN A 622 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS A 864 GLN ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 HIS ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 821 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22601 Z= 0.347 Angle : 0.931 11.722 30696 Z= 0.486 Chirality : 0.049 0.268 3531 Planarity : 0.005 0.055 3910 Dihedral : 7.152 41.867 3211 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.22 % Favored : 89.30 % Rotamer: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.76 % Twisted Proline : 1.85 % Twisted General : 0.74 % 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: -2.42 (0.17), residues: 2496 helix: -0.49 (0.13), residues: 1576 sheet: None (None), residues: 0 loop : -3.66 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 401 HIS 0.008 0.002 HIS B 825 PHE 0.034 0.003 PHE A 815 TYR 0.029 0.002 TYR C 546 ARG 0.011 0.001 ARG D 383 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 551 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 MET cc_start: 0.7984 (tpp) cc_final: 0.7517 (tpp) REVERT: A 622 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7677 (t0) REVERT: A 646 MET cc_start: 0.8602 (ppp) cc_final: 0.8365 (ppp) REVERT: A 649 LYS cc_start: 0.8538 (ttmm) cc_final: 0.7315 (tptt) REVERT: A 713 ASP cc_start: 0.8036 (m-30) cc_final: 0.6942 (t0) REVERT: A 731 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8257 (tm-30) REVERT: A 756 GLN cc_start: 0.8801 (pt0) cc_final: 0.8148 (pp30) REVERT: A 825 HIS cc_start: 0.6741 (m-70) cc_final: 0.5617 (m-70) REVERT: A 829 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8271 (mt-10) REVERT: B 125 ILE cc_start: 0.8949 (mm) cc_final: 0.8527 (mt) REVERT: B 303 MET cc_start: 0.9130 (ttt) cc_final: 0.8404 (ttm) REVERT: B 526 PHE cc_start: 0.8050 (t80) cc_final: 0.7788 (t80) REVERT: B 556 ARG cc_start: 0.6019 (mmt90) cc_final: 0.5628 (mtt180) REVERT: B 622 ASN cc_start: 0.8043 (t0) cc_final: 0.7433 (t0) REVERT: B 649 LYS cc_start: 0.8938 (tptp) cc_final: 0.8635 (tptt) REVERT: B 654 MET cc_start: 0.7804 (ptm) cc_final: 0.7579 (ptm) REVERT: B 713 ASP cc_start: 0.7927 (m-30) cc_final: 0.7004 (t0) REVERT: B 739 TYR cc_start: 0.7558 (t80) cc_final: 0.6939 (t80) REVERT: B 756 GLN cc_start: 0.8637 (pt0) cc_final: 0.8139 (pp30) REVERT: B 830 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8188 (tm-30) REVERT: C 232 ASN cc_start: 0.7602 (m-40) cc_final: 0.7297 (m-40) REVERT: C 556 ARG cc_start: 0.7893 (tpp80) cc_final: 0.6814 (mmt90) REVERT: C 649 LYS cc_start: 0.8534 (mttm) cc_final: 0.7374 (tptt) REVERT: C 654 MET cc_start: 0.8230 (ptm) cc_final: 0.7323 (ttp) REVERT: C 693 HIS cc_start: 0.8394 (t-90) cc_final: 0.8143 (t-170) REVERT: C 756 GLN cc_start: 0.8820 (pt0) cc_final: 0.8076 (pp30) REVERT: C 776 TYR cc_start: 0.7709 (p90) cc_final: 0.6789 (p90) REVERT: C 830 GLN cc_start: 0.8758 (tt0) cc_final: 0.8329 (tm-30) REVERT: D 589 PHE cc_start: 0.8548 (t80) cc_final: 0.8177 (t80) REVERT: D 622 ASN cc_start: 0.8288 (t0) cc_final: 0.7855 (t0) REVERT: D 649 LYS cc_start: 0.8351 (ttmm) cc_final: 0.7506 (tptt) REVERT: D 756 GLN cc_start: 0.8807 (pt0) cc_final: 0.8248 (pp30) REVERT: D 776 TYR cc_start: 0.7452 (p90) cc_final: 0.6699 (p90) REVERT: D 829 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8366 (mt-10) outliers start: 2 outliers final: 0 residues processed: 551 average time/residue: 0.3167 time to fit residues: 272.9145 Evaluate side-chains 477 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 476 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 247 optimal weight: 20.0000 chunk 164 optimal weight: 0.9990 chunk 293 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN A 864 GLN ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 ASN D 744 ASN D 751 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22601 Z= 0.237 Angle : 0.846 12.148 30696 Z= 0.442 Chirality : 0.045 0.257 3531 Planarity : 0.004 0.062 3910 Dihedral : 6.749 39.046 3211 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.90 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.92 % Twisted Proline : 2.78 % Twisted General : 0.33 % 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: -2.06 (0.17), residues: 2496 helix: -0.18 (0.14), residues: 1552 sheet: None (None), residues: 0 loop : -3.49 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 401 HIS 0.008 0.001 HIS B 825 PHE 0.041 0.002 PHE A 234 TYR 0.018 0.001 TYR C 546 ARG 0.007 0.001 ARG D 629 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.7384 (mtt180) cc_final: 0.6563 (mtt180) REVERT: A 245 MET cc_start: 0.7609 (tpp) cc_final: 0.7370 (tpp) REVERT: A 622 ASN cc_start: 0.7805 (t0) cc_final: 0.7446 (t0) REVERT: A 646 MET cc_start: 0.8629 (ppp) cc_final: 0.8343 (ppp) REVERT: A 649 LYS cc_start: 0.8460 (ttmm) cc_final: 0.7311 (tptt) REVERT: A 713 ASP cc_start: 0.7925 (m-30) cc_final: 0.6934 (t0) REVERT: A 756 GLN cc_start: 0.8749 (pt0) cc_final: 0.8179 (pp30) REVERT: A 825 HIS cc_start: 0.6676 (m-70) cc_final: 0.5641 (m-70) REVERT: A 829 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8181 (mt-10) REVERT: A 830 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8136 (tm-30) REVERT: B 125 ILE cc_start: 0.8846 (mm) cc_final: 0.8446 (mt) REVERT: B 556 ARG cc_start: 0.5917 (mmt90) cc_final: 0.5688 (mmt90) REVERT: B 649 LYS cc_start: 0.8805 (tptp) cc_final: 0.8603 (tptt) REVERT: B 654 MET cc_start: 0.7545 (ptm) cc_final: 0.7241 (ptm) REVERT: B 713 ASP cc_start: 0.7885 (m-30) cc_final: 0.6932 (t0) REVERT: B 756 GLN cc_start: 0.8642 (pt0) cc_final: 0.8112 (pp30) REVERT: B 829 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8056 (mt-10) REVERT: B 830 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8192 (tm-30) REVERT: C 207 SER cc_start: 0.8613 (p) cc_final: 0.8056 (t) REVERT: C 297 GLN cc_start: 0.8314 (tp40) cc_final: 0.7371 (tp40) REVERT: C 556 ARG cc_start: 0.7854 (tpp80) cc_final: 0.6852 (mmt90) REVERT: C 578 PHE cc_start: 0.7552 (m-10) cc_final: 0.7293 (m-10) REVERT: C 649 LYS cc_start: 0.8468 (mttm) cc_final: 0.7588 (tptt) REVERT: C 654 MET cc_start: 0.7998 (ptm) cc_final: 0.7454 (ptm) REVERT: C 756 GLN cc_start: 0.8811 (pt0) cc_final: 0.8203 (pp30) REVERT: C 776 TYR cc_start: 0.7431 (p90) cc_final: 0.6614 (p90) REVERT: D 297 GLN cc_start: 0.8353 (tp40) cc_final: 0.7486 (tp40) REVERT: D 532 MET cc_start: 0.7829 (tpt) cc_final: 0.7286 (tpp) REVERT: D 622 ASN cc_start: 0.8056 (t0) cc_final: 0.7676 (t0) REVERT: D 649 LYS cc_start: 0.8337 (ttmm) cc_final: 0.7496 (tptt) REVERT: D 776 TYR cc_start: 0.7415 (p90) cc_final: 0.6615 (p90) REVERT: D 829 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8351 (mt-10) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.3174 time to fit residues: 269.7877 Evaluate side-chains 460 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 199 optimal weight: 0.2980 chunk 144 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 744 ASN A 751 ASN A 864 GLN B 751 ASN C 751 ASN ** C 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.6868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22601 Z= 0.205 Angle : 0.821 12.279 30696 Z= 0.431 Chirality : 0.045 0.262 3531 Planarity : 0.004 0.052 3910 Dihedral : 6.450 38.243 3211 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.94 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.88 % Twisted Proline : 2.78 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2496 helix: 0.02 (0.14), residues: 1516 sheet: None (None), residues: 0 loop : -3.22 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 401 HIS 0.007 0.001 HIS B 825 PHE 0.030 0.002 PHE C 234 TYR 0.030 0.001 TYR C 336 ARG 0.004 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6596 (mtt180) REVERT: A 245 MET cc_start: 0.7666 (tpp) cc_final: 0.7434 (tpp) REVERT: A 295 LEU cc_start: 0.8918 (mt) cc_final: 0.8692 (mt) REVERT: A 526 PHE cc_start: 0.7868 (t80) cc_final: 0.7499 (t80) REVERT: A 556 ARG cc_start: 0.4870 (mtt180) cc_final: 0.4667 (mtt180) REVERT: A 622 ASN cc_start: 0.7703 (t0) cc_final: 0.7491 (t0) REVERT: A 646 MET cc_start: 0.8551 (ppp) cc_final: 0.8312 (ppp) REVERT: A 649 LYS cc_start: 0.8447 (ttmm) cc_final: 0.7314 (tptt) REVERT: A 713 ASP cc_start: 0.7961 (m-30) cc_final: 0.6944 (t0) REVERT: A 756 GLN cc_start: 0.8681 (pt0) cc_final: 0.8108 (pp30) REVERT: A 776 TYR cc_start: 0.7037 (p90) cc_final: 0.6542 (p90) REVERT: A 825 HIS cc_start: 0.6692 (m-70) cc_final: 0.5737 (m-70) REVERT: A 829 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 830 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 864 GLN cc_start: 0.8674 (tt0) cc_final: 0.8317 (tt0) REVERT: B 125 ILE cc_start: 0.8783 (mm) cc_final: 0.8443 (mt) REVERT: B 245 MET cc_start: 0.7795 (tpp) cc_final: 0.7582 (tpp) REVERT: B 556 ARG cc_start: 0.5923 (mmt90) cc_final: 0.5496 (mtt180) REVERT: B 654 MET cc_start: 0.7424 (ptm) cc_final: 0.7060 (ptm) REVERT: B 713 ASP cc_start: 0.7849 (m-30) cc_final: 0.6930 (t0) REVERT: B 756 GLN cc_start: 0.8605 (pt0) cc_final: 0.8062 (pp30) REVERT: B 776 TYR cc_start: 0.6837 (p90) cc_final: 0.6508 (p90) REVERT: B 830 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 859 GLU cc_start: 0.8265 (tp30) cc_final: 0.7497 (tm-30) REVERT: C 297 GLN cc_start: 0.8356 (tp40) cc_final: 0.7448 (tp40) REVERT: C 556 ARG cc_start: 0.7855 (tpp80) cc_final: 0.6946 (mmt90) REVERT: C 571 LYS cc_start: 0.7287 (mttp) cc_final: 0.6951 (tptt) REVERT: C 578 PHE cc_start: 0.7637 (m-10) cc_final: 0.7055 (m-80) REVERT: C 649 LYS cc_start: 0.8319 (mttm) cc_final: 0.7645 (tptt) REVERT: C 654 MET cc_start: 0.7835 (ptm) cc_final: 0.7399 (ptm) REVERT: C 673 LYS cc_start: 0.9199 (mtpp) cc_final: 0.8972 (mmtt) REVERT: C 756 GLN cc_start: 0.8808 (pt0) cc_final: 0.8136 (pp30) REVERT: D 213 ARG cc_start: 0.7257 (mtt180) cc_final: 0.6529 (mtt180) REVERT: D 297 GLN cc_start: 0.8350 (tp40) cc_final: 0.7488 (tp40) REVERT: D 377 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8315 (mtmt) REVERT: D 532 MET cc_start: 0.7761 (tpt) cc_final: 0.7089 (tpp) REVERT: D 629 ARG cc_start: 0.7646 (tpt-90) cc_final: 0.7303 (tpt-90) REVERT: D 713 ASP cc_start: 0.6876 (t70) cc_final: 0.6657 (t70) REVERT: D 776 TYR cc_start: 0.7266 (p90) cc_final: 0.6511 (p90) REVERT: D 829 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8279 (mt-10) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.3095 time to fit residues: 266.7372 Evaluate side-chains 471 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 20.0000 chunk 280 optimal weight: 0.7980 chunk 256 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 258 optimal weight: 0.9990 chunk 272 optimal weight: 0.0010 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN C 231 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 HIS D 622 ASN ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22601 Z= 0.230 Angle : 0.828 12.161 30696 Z= 0.432 Chirality : 0.045 0.269 3531 Planarity : 0.004 0.081 3910 Dihedral : 6.469 36.178 3211 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.66 % Favored : 89.94 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.88 % Twisted Proline : 1.85 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.17), residues: 2496 helix: 0.12 (0.14), residues: 1580 sheet: None (None), residues: 0 loop : -3.43 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 401 HIS 0.008 0.001 HIS B 825 PHE 0.027 0.002 PHE C 512 TYR 0.021 0.001 TYR C 546 ARG 0.006 0.000 ARG B 857 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 2.346 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 213 ARG cc_start: 0.7222 (mtt180) cc_final: 0.6658 (mtt180) REVERT: A 556 ARG cc_start: 0.4915 (mtt180) cc_final: 0.4650 (mtt180) REVERT: A 622 ASN cc_start: 0.7756 (t0) cc_final: 0.7465 (t0) REVERT: A 649 LYS cc_start: 0.8497 (ttmm) cc_final: 0.7620 (tptt) REVERT: A 654 MET cc_start: 0.7760 (ptm) cc_final: 0.6925 (ptm) REVERT: A 713 ASP cc_start: 0.8009 (m-30) cc_final: 0.6941 (t0) REVERT: A 756 GLN cc_start: 0.8695 (pt0) cc_final: 0.8107 (pp30) REVERT: A 776 TYR cc_start: 0.6960 (p90) cc_final: 0.6510 (p90) REVERT: A 825 HIS cc_start: 0.6702 (m-70) cc_final: 0.6159 (m-70) REVERT: A 859 GLU cc_start: 0.8519 (tp30) cc_final: 0.7321 (tm-30) REVERT: B 125 ILE cc_start: 0.8803 (mm) cc_final: 0.8488 (mt) REVERT: B 286 MET cc_start: 0.8335 (tpt) cc_final: 0.8123 (mmm) REVERT: B 556 ARG cc_start: 0.6004 (mmt90) cc_final: 0.5601 (mtt180) REVERT: B 622 ASN cc_start: 0.8104 (t0) cc_final: 0.7732 (t0) REVERT: B 654 MET cc_start: 0.7364 (ptm) cc_final: 0.7135 (ptm) REVERT: B 713 ASP cc_start: 0.7810 (m-30) cc_final: 0.6933 (t0) REVERT: B 756 GLN cc_start: 0.8634 (pt0) cc_final: 0.8147 (pp30) REVERT: B 776 TYR cc_start: 0.6980 (p90) cc_final: 0.6583 (p90) REVERT: B 859 GLU cc_start: 0.8288 (tp30) cc_final: 0.7559 (tm-30) REVERT: C 297 GLN cc_start: 0.8256 (tp40) cc_final: 0.7372 (tp40) REVERT: C 303 MET cc_start: 0.8569 (ttt) cc_final: 0.8264 (ttt) REVERT: C 556 ARG cc_start: 0.7822 (tpp80) cc_final: 0.6768 (mmt90) REVERT: C 649 LYS cc_start: 0.8272 (mttm) cc_final: 0.7533 (tptt) REVERT: C 654 MET cc_start: 0.7893 (ptm) cc_final: 0.7506 (ptm) REVERT: C 756 GLN cc_start: 0.8817 (pt0) cc_final: 0.8130 (pp30) REVERT: D 213 ARG cc_start: 0.7175 (mtt180) cc_final: 0.6536 (mtt180) REVERT: D 245 MET cc_start: 0.7713 (tpp) cc_final: 0.7341 (tpp) REVERT: D 297 GLN cc_start: 0.8334 (tp40) cc_final: 0.7401 (tp40) REVERT: D 349 GLU cc_start: 0.7707 (pt0) cc_final: 0.7468 (pt0) REVERT: D 532 MET cc_start: 0.7911 (tpt) cc_final: 0.7146 (tpp) REVERT: D 556 ARG cc_start: 0.5543 (mmt90) cc_final: 0.5205 (mtt180) REVERT: D 713 ASP cc_start: 0.6925 (t70) cc_final: 0.6701 (t70) REVERT: D 776 TYR cc_start: 0.7321 (p90) cc_final: 0.6593 (p90) REVERT: D 829 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8373 (mt-10) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.3024 time to fit residues: 251.8376 Evaluate side-chains 444 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.6980 chunk 288 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 302 optimal weight: 8.9990 chunk 278 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 25 optimal weight: 0.1980 chunk 186 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN B 406 ASN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN ** D 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22601 Z= 0.201 Angle : 0.805 12.322 30696 Z= 0.421 Chirality : 0.044 0.256 3531 Planarity : 0.004 0.070 3910 Dihedral : 6.277 33.829 3211 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.50 % Favored : 89.14 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.88 % Twisted Proline : 1.85 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.17), residues: 2496 helix: 0.24 (0.14), residues: 1556 sheet: None (None), residues: 0 loop : -3.34 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 401 HIS 0.008 0.001 HIS B 825 PHE 0.022 0.002 PHE D 750 TYR 0.019 0.001 TYR C 546 ARG 0.012 0.001 ARG A 629 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 2.426 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: A 213 ARG cc_start: 0.7211 (mtt180) cc_final: 0.6721 (mtt180) REVERT: A 556 ARG cc_start: 0.4917 (mtt180) cc_final: 0.4641 (mtt180) REVERT: A 622 ASN cc_start: 0.7795 (t0) cc_final: 0.7558 (t0) REVERT: A 649 LYS cc_start: 0.8406 (ttmm) cc_final: 0.7522 (tptt) REVERT: A 654 MET cc_start: 0.7597 (ptm) cc_final: 0.6824 (ptm) REVERT: A 713 ASP cc_start: 0.7991 (m-30) cc_final: 0.6976 (t0) REVERT: A 756 GLN cc_start: 0.8666 (pt0) cc_final: 0.8105 (pp30) REVERT: A 776 TYR cc_start: 0.6852 (p90) cc_final: 0.6486 (p90) REVERT: A 825 HIS cc_start: 0.6737 (m-70) cc_final: 0.6170 (m-70) REVERT: B 125 ILE cc_start: 0.8767 (mm) cc_final: 0.8458 (mt) REVERT: B 245 MET cc_start: 0.7832 (tpp) cc_final: 0.7618 (tpp) REVERT: B 556 ARG cc_start: 0.6061 (mmt90) cc_final: 0.5489 (mtt180) REVERT: B 713 ASP cc_start: 0.7815 (m-30) cc_final: 0.6935 (t0) REVERT: B 756 GLN cc_start: 0.8655 (pt0) cc_final: 0.8159 (pp30) REVERT: B 776 TYR cc_start: 0.6832 (p90) cc_final: 0.6531 (p90) REVERT: C 297 GLN cc_start: 0.8270 (tp40) cc_final: 0.7412 (tp40) REVERT: C 303 MET cc_start: 0.8745 (ttt) cc_final: 0.8105 (ttm) REVERT: C 526 PHE cc_start: 0.7037 (t80) cc_final: 0.6490 (m-80) REVERT: C 556 ARG cc_start: 0.7762 (tpp80) cc_final: 0.6704 (mmt90) REVERT: C 649 LYS cc_start: 0.8047 (mttm) cc_final: 0.7272 (tptt) REVERT: C 654 MET cc_start: 0.7777 (ptm) cc_final: 0.7413 (ptm) REVERT: C 713 ASP cc_start: 0.7764 (m-30) cc_final: 0.7153 (t0) REVERT: C 756 GLN cc_start: 0.8798 (pt0) cc_final: 0.8104 (pp30) REVERT: D 213 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6590 (mtt180) REVERT: D 297 GLN cc_start: 0.8298 (tp40) cc_final: 0.7401 (tp40) REVERT: D 349 GLU cc_start: 0.7813 (pt0) cc_final: 0.7576 (pt0) REVERT: D 522 MET cc_start: 0.7905 (mtt) cc_final: 0.7673 (mtt) REVERT: D 526 PHE cc_start: 0.7693 (t80) cc_final: 0.7365 (t80) REVERT: D 532 MET cc_start: 0.7915 (tpt) cc_final: 0.7424 (tpp) REVERT: D 776 TYR cc_start: 0.7118 (p90) cc_final: 0.6545 (p90) REVERT: D 829 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8303 (mt-10) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.3008 time to fit residues: 248.4200 Evaluate side-chains 439 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 5.9990 chunk 256 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN ** D 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.182130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.154441 restraints weight = 36556.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.157391 restraints weight = 23082.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.159403 restraints weight = 16415.712| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.7384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22601 Z= 0.237 Angle : 0.831 12.687 30696 Z= 0.434 Chirality : 0.045 0.222 3531 Planarity : 0.004 0.064 3910 Dihedral : 6.363 33.395 3211 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.30 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.88 % Twisted Proline : 0.93 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.17), residues: 2496 helix: 0.19 (0.14), residues: 1588 sheet: None (None), residues: 0 loop : -3.51 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 401 HIS 0.007 0.001 HIS B 825 PHE 0.039 0.002 PHE D 750 TYR 0.024 0.001 TYR C 546 ARG 0.010 0.001 ARG C 629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5195.34 seconds wall clock time: 94 minutes 13.01 seconds (5653.01 seconds total)