Starting phenix.real_space_refine on Thu Jun 19 04:00:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e96_27957/06_2025/8e96_27957.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e96_27957/06_2025/8e96_27957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e96_27957/06_2025/8e96_27957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e96_27957/06_2025/8e96_27957.map" model { file = "/net/cci-nas-00/data/ceres_data/8e96_27957/06_2025/8e96_27957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e96_27957/06_2025/8e96_27957.cif" } resolution = 3.38 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= 0.006 sd= 0.021 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 97 5.16 5 C 13914 2.51 5 N 3830 2.21 5 O 4083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21924 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5695 Classifications: {'peptide': 738} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 31, 'TRANS': 706} Chain breaks: 4 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 5229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5229 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 651} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 5606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5606 Classifications: {'peptide': 721} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 30, 'TRANS': 690} Chain breaks: 5 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "D" Number of atoms: 5280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5280 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 656} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.18, per 1000 atoms: 0.60 Number of scatterers: 21924 At special positions: 0 Unit cell: (119.84, 145.52, 177.192, 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 97 16.00 O 4083 8.00 N 3830 7.00 C 13914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 455 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 348 " distance=2.03 Simple disulfide: pdb=" SG CYS D 455 " - pdb=" SG CYS D 483 " distance=2.03 Simple disulfide: pdb=" SG CYS D 462 " - pdb=" SG CYS D 484 " distance=2.03 Simple disulfide: pdb=" SG CYS D 773 " - pdb=" SG CYS D 828 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 902 " - " ASN A 771 " " NAG B 902 " - " ASN B 715 " " NAG C 902 " - " ASN C 276 " " NAG C 903 " - " ASN C 350 " " NAG C 904 " - " ASN C 771 " " NAG D 902 " - " ASN D 715 " Time building additional restraints: 4.63 Conformation dependent library (CDL) restraints added in 2.7 seconds 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5264 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 34 sheets defined 39.7% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.558A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 42 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 removed outlier: 3.503A pdb=" N VAL A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 Processing helix chain 'A' and resid 103 through 111 removed outlier: 4.046A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 146 through 158 removed outlier: 4.126A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.562A pdb=" N LEU A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 205 through 212 removed outlier: 3.637A pdb=" N GLU A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.930A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 4.051A pdb=" N ARG A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 261 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.634A pdb=" N GLN A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.610A pdb=" N LYS A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.788A pdb=" N LEU A 463 " --> pdb=" O CYS A 459 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.077A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.746A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 582 removed outlier: 3.861A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.739A pdb=" N PHE A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 655 removed outlier: 4.134A pdb=" N VAL A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TRP A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.506A pdb=" N ARG A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.820A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 735 through 743 removed outlier: 3.802A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 removed outlier: 3.948A pdb=" N LYS A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 792 removed outlier: 3.862A pdb=" N ASP A 789 " --> pdb=" O MET A 785 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS A 790 " --> pdb=" O GLU A 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.757A pdb=" N ALA B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 59 through 65' Processing helix chain 'B' and resid 68 through 77 removed outlier: 4.050A pdb=" N ALA B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 108 removed outlier: 4.276A pdb=" N GLN B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS B 104 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.752A pdb=" N LEU B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 173 through 182 removed outlier: 3.510A pdb=" N LEU B 179 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 209 removed outlier: 3.703A pdb=" N PHE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 207 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.925A pdb=" N VAL B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 314 removed outlier: 3.910A pdb=" N ASP B 314 " --> pdb=" O GLY B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 311 through 314' Processing helix chain 'B' and resid 315 through 330 removed outlier: 3.759A pdb=" N VAL B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 338 removed outlier: 4.069A pdb=" N LEU B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 4.369A pdb=" N ARG B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 499 removed outlier: 3.510A pdb=" N ILE B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 530 Processing helix chain 'B' and resid 543 through 548 removed outlier: 3.666A pdb=" N GLU B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 641 removed outlier: 3.532A pdb=" N VAL B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE B 641 " --> pdb=" O TRP B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 681 removed outlier: 3.538A pdb=" N VAL B 659 " --> pdb=" O SER B 655 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 666 " --> pdb=" O TRP B 662 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 668 " --> pdb=" O PHE B 664 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN B 676 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET B 681 " --> pdb=" O LEU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.886A pdb=" N GLN B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 705 removed outlier: 3.791A pdb=" N GLN B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 724 Processing helix chain 'B' and resid 726 through 734 removed outlier: 4.086A pdb=" N SER B 731 " --> pdb=" O PRO B 727 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR B 732 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 733 " --> pdb=" O MET B 729 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 734 " --> pdb=" O HIS B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 751 removed outlier: 3.807A pdb=" N THR B 746 " --> pdb=" O GLU B 742 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 799 through 813 removed outlier: 3.649A pdb=" N LEU B 805 " --> pdb=" O ARG B 801 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 Processing helix chain 'B' and resid 848 through 862 removed outlier: 3.700A pdb=" N LEU B 861 " --> pdb=" O GLY B 857 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.505A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.582A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.817A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.557A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 226 through 238 removed outlier: 3.661A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 7.327A pdb=" N GLY C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN C 257 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 294 removed outlier: 3.633A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 321 through 327 Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.804A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 506 removed outlier: 3.622A pdb=" N LEU C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.555A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 removed outlier: 3.787A pdb=" N VAL C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 567 " --> pdb=" O TRP C 563 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 575 " --> pdb=" O HIS C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 607 removed outlier: 3.828A pdb=" N ALA C 606 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 615 removed outlier: 3.876A pdb=" N LEU C 615 " --> pdb=" O TRP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 655 removed outlier: 3.646A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 639 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET C 641 " --> pdb=" O ALA C 637 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 647 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 651 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 652 " --> pdb=" O THR C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.541A pdb=" N ARG C 673 " --> pdb=" O ASP C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 693 Processing helix chain 'C' and resid 694 through 695 No H-bonds generated for 'chain 'C' and resid 694 through 695' Processing helix chain 'C' and resid 696 through 700 Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.678A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 744 removed outlier: 4.184A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.511A pdb=" N VAL C 772 " --> pdb=" O TRP C 768 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.526A pdb=" N ASP C 789 " --> pdb=" O MET C 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 97 through 110 removed outlier: 3.514A pdb=" N GLY D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 126 through 136 removed outlier: 3.635A pdb=" N LEU D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D 136 " --> pdb=" O PHE D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.802A pdb=" N LEU D 150 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 196 through 209 removed outlier: 3.513A pdb=" N SER D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 207 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.511A pdb=" N LEU D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 263 removed outlier: 3.723A pdb=" N ALA D 263 " --> pdb=" O ALA D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 338 removed outlier: 3.875A pdb=" N ALA D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 333 " --> pdb=" O ARG D 329 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG D 336 " --> pdb=" O GLN D 332 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 364 removed outlier: 3.867A pdb=" N HIS D 361 " --> pdb=" O GLU D 358 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARG D 362 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 removed outlier: 3.515A pdb=" N ILE D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS D 497 " --> pdb=" O LYS D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 530 removed outlier: 3.690A pdb=" N TYR D 530 " --> pdb=" O GLY D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 548 removed outlier: 3.564A pdb=" N GLU D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 677 removed outlier: 4.147A pdb=" N LEU D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL D 661 " --> pdb=" O ILE D 657 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE D 665 " --> pdb=" O VAL D 661 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA D 666 " --> pdb=" O TRP D 662 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D 668 " --> pdb=" O PHE D 664 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 680 No H-bonds generated for 'chain 'D' and resid 678 through 680' Processing helix chain 'D' and resid 695 through 700 removed outlier: 3.541A pdb=" N GLN D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 726 Processing helix chain 'D' and resid 726 through 734 removed outlier: 3.511A pdb=" N HIS D 730 " --> pdb=" O TYR D 726 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 731 " --> pdb=" O PRO D 727 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR D 732 " --> pdb=" O ASP D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 737 No H-bonds generated for 'chain 'D' and resid 735 through 737' Processing helix chain 'D' and resid 740 through 750 removed outlier: 3.702A pdb=" N THR D 746 " --> pdb=" O GLU D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 769 Processing helix chain 'D' and resid 770 through 773 Processing helix chain 'D' and resid 799 through 813 removed outlier: 3.559A pdb=" N LEU D 805 " --> pdb=" O ARG D 801 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 806 " --> pdb=" O PRO D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 824 Processing helix chain 'D' and resid 847 through 862 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 62 removed outlier: 7.692A pdb=" N TYR A 88 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.453A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 271 removed outlier: 6.332A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 413 removed outlier: 6.700A pdb=" N ILE A 435 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU A 478 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR A 437 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA6, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.480A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.870A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 91 removed outlier: 6.419A pdb=" N LEU B 55 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 91 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE B 57 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA B 54 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 142 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE B 141 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 216 through 222 removed outlier: 8.475A pdb=" N PHE B 187 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N LEU B 221 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 189 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE B 243 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 273 " --> pdb=" O ARG B 244 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 246 " --> pdb=" O PHE B 273 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL B 307 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B 306 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 388 " --> pdb=" O ARG B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 367 through 369 Processing sheet with id=AB1, first strand: chain 'B' and resid 502 through 507 Processing sheet with id=AB2, first strand: chain 'B' and resid 444 through 446 removed outlier: 3.728A pdb=" N CYS B 483 " --> pdb=" O GLU B 446 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 515 through 517 Processing sheet with id=AB4, first strand: chain 'B' and resid 551 through 552 Processing sheet with id=AB5, first strand: chain 'B' and resid 756 through 758 Processing sheet with id=AB6, first strand: chain 'B' and resid 756 through 758 removed outlier: 6.672A pdb=" N THR B 559 " --> pdb=" O THR B 786 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR B 786 " --> pdb=" O THR B 559 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 64 through 66 removed outlier: 6.673A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU C 121 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL C 92 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 196 through 197 removed outlier: 7.751A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 267 through 268 removed outlier: 3.680A pdb=" N GLY C 268 " --> pdb=" O MET C 354 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 473 through 478 removed outlier: 6.930A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 411 through 413 removed outlier: 3.540A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 487 through 488 removed outlier: 3.708A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 527 through 528 Processing sheet with id=AC5, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AC6, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.993A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AC8, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.823A pdb=" N ALA D 54 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL D 115 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 216 through 222 removed outlier: 7.974A pdb=" N PHE D 187 " --> pdb=" O GLY D 219 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N LEU D 221 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA D 189 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 243 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 244 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL D 307 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU D 304 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 368 through 369 Processing sheet with id=AD2, first strand: chain 'D' and resid 402 through 405 removed outlier: 3.887A pdb=" N ARG D 410 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 434 through 435 removed outlier: 3.515A pdb=" N ALA D 435 " --> pdb=" O MET D 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 444 through 447 Processing sheet with id=AD5, first strand: chain 'D' and resid 516 through 517 Processing sheet with id=AD6, first strand: chain 'D' and resid 756 through 758 Processing sheet with id=AD7, first strand: chain 'D' and resid 756 through 758 removed outlier: 4.732A pdb=" N ILE D 561 " --> pdb=" O ALA D 785 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ALA D 785 " --> pdb=" O ILE D 561 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1836 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: 7.11 Time building geometry restraints manager: 5.61 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: 7255 1.34 - 1.46: 5054 1.46 - 1.58: 9918 1.58 - 1.70: 0 1.70 - 1.82: 157 Bond restraints: 22384 Sorted by residual: bond pdb=" C1 NAG D 902 " pdb=" O5 NAG D 902 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C1 NAG C 903 " pdb=" O5 NAG C 903 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.84e+00 bond pdb=" C THR A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.83e+00 bond pdb=" C1 NAG C 902 " pdb=" O5 NAG C 902 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C5 NAG C 904 " pdb=" O5 NAG C 904 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.63e+00 ... (remaining 22379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 29878 1.88 - 3.77: 422 3.77 - 5.65: 56 5.65 - 7.54: 9 7.54 - 9.42: 3 Bond angle restraints: 30368 Sorted by residual: angle pdb=" N PRO D 477 " pdb=" CA PRO D 477 " pdb=" CB PRO D 477 " ideal model delta sigma weight residual 103.00 110.40 -7.40 1.10e+00 8.26e-01 4.53e+01 angle pdb=" N VAL B 426 " pdb=" CA VAL B 426 " pdb=" C VAL B 426 " ideal model delta sigma weight residual 112.80 109.01 3.79 1.15e+00 7.56e-01 1.08e+01 angle pdb=" CB MET C 125 " pdb=" CG MET C 125 " pdb=" SD MET C 125 " ideal model delta sigma weight residual 112.70 122.12 -9.42 3.00e+00 1.11e-01 9.87e+00 angle pdb=" C PHE A 533 " pdb=" CA PHE A 533 " pdb=" CB PHE A 533 " ideal model delta sigma weight residual 110.95 106.12 4.83 1.55e+00 4.16e-01 9.71e+00 angle pdb=" N VAL A 204 " pdb=" CA VAL A 204 " pdb=" C VAL A 204 " ideal model delta sigma weight residual 111.88 108.89 2.99 1.06e+00 8.90e-01 7.97e+00 ... (remaining 30363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 11976 17.65 - 35.30: 1196 35.30 - 52.95: 225 52.95 - 70.60: 35 70.60 - 88.25: 22 Dihedral angle restraints: 13454 sinusoidal: 5293 harmonic: 8161 Sorted by residual: dihedral pdb=" CB CYS D 462 " pdb=" SG CYS D 462 " pdb=" SG CYS D 484 " pdb=" CB CYS D 484 " ideal model delta sinusoidal sigma weight residual -86.00 -172.09 86.09 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS B 462 " pdb=" SG CYS B 462 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual -86.00 -159.46 73.46 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS B 455 " pdb=" SG CYS B 455 " pdb=" SG CYS B 483 " pdb=" CB CYS B 483 " ideal model delta sinusoidal sigma weight residual 93.00 164.60 -71.60 1 1.00e+01 1.00e-02 6.57e+01 ... (remaining 13451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3171 0.086 - 0.172: 253 0.172 - 0.258: 5 0.258 - 0.345: 0 0.345 - 0.431: 1 Chirality restraints: 3430 Sorted by residual: chirality pdb=" C1 NAG C 904 " pdb=" ND2 ASN C 771 " pdb=" C2 NAG C 904 " pdb=" O5 NAG C 904 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA PRO D 477 " pdb=" N PRO D 477 " pdb=" C PRO D 477 " pdb=" CB PRO D 477 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL C 426 " pdb=" CA VAL C 426 " pdb=" CG1 VAL C 426 " pdb=" CG2 VAL C 426 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3427 not shown) Planarity restraints: 3924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 315 " 0.018 2.00e-02 2.50e+03 1.51e-02 5.71e+00 pdb=" CG TRP A 315 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 315 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 315 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 315 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 315 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 315 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 315 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 315 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 315 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 700 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO D 701 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 701 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 701 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 715 " 0.022 2.00e-02 2.50e+03 2.05e-02 5.26e+00 pdb=" CG ASN D 715 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN D 715 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 715 " -0.014 2.00e-02 2.50e+03 pdb=" C1 NAG D 902 " 0.018 2.00e-02 2.50e+03 ... (remaining 3921 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 528 2.70 - 3.25: 21623 3.25 - 3.80: 31826 3.80 - 4.35: 40832 4.35 - 4.90: 68133 Nonbonded interactions: 162942 Sorted by model distance: nonbonded pdb=" O HIS B 794 " pdb=" OG SER B 797 " model vdw 2.149 3.040 nonbonded pdb=" NE2 GLN C 86 " pdb=" O PRO C 304 " model vdw 2.192 3.120 nonbonded pdb=" OD2 ASP D 759 " pdb=" OH TYR D 789 " model vdw 2.215 3.040 nonbonded pdb=" O GLU D 405 " pdb=" OG1 THR D 408 " model vdw 2.216 3.040 nonbonded pdb=" OG SER D 166 " pdb=" OE1 GLN D 171 " model vdw 2.230 3.040 ... (remaining 162937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 322 or (resid 323 and (name N or name CA or name C or nam \ e O or name CB )) or resid 324 through 439 or resid 449 through 489 or resid 496 \ through 547 or resid 549 or (resid 554 and (name N or name CA or name C or name \ O or name CB )) or resid 560 through 568 or (resid 569 through 577 and (name N \ or name CA or name C or name O or name CB )) or resid 603 through 617 or (resid \ 626 through 627 and (name N or name CA or name C or name O or name CB )) or resi \ d 628 through 630 or (resid 631 through 632 and (name N or name CA or name C or \ name O or name CB )) or resid 633 or (resid 634 and (name N or name CA or name C \ or name O or name CB )) or resid 635 through 654 or (resid 655 and (name N or n \ ame CA or name C or name O or name CB )) or resid 656 through 796 or resid 902)) \ selection = (chain 'C' and (resid 25 through 547 or (resid 553 and (name N or name CA or nam \ e C or name O or name CB )) or resid 558 or (resid 560 and (name N or name CA or \ name C or name O or name CB )) or resid 561 or (resid 562 through 566 and (name \ N or name CA or name C or name O or name CB )) or (resid 567 through 603 and (n \ ame N or name CA or name C or name O or name CB )) or resid 604 through 609 or ( \ resid 610 through 611 and (name N or name CA or name C or name O or name CB )) o \ r resid 612 through 617 or resid 626 through 653 or (resid 654 through 655 and ( \ name N or name CA or name C or name O or name CB )) or resid 656 or (resid 657 t \ hrough 659 and (name N or name CA or name C or name O or name CB )) or resid 660 \ or (resid 661 through 662 and (name N or name CA or name C or name O or name CB \ )) or resid 663 through 677 or (resid 678 and (name N or name CA or name C or n \ ame O or name CB )) or resid 679 through 724 or (resid 725 and (name N or name C \ A or name C or name O or name CB )) or resid 726 through 796 or resid 904)) } ncs_group { reference = (chain 'B' and ((resid 48 through 49 and (name N or name CA or name C or name O \ or name CB )) or resid 50 through 217 or (resid 218 and (name N or name CA or na \ me C or name O or name CB )) or resid 219 through 478 or (resid 479 and (name N \ or name CA or name C or name O or name CB )) or resid 480 through 568 or resid 6 \ 52 or (resid 653 through 658 and (name N or name CA or name C or name O or name \ CB )) or resid 659 or (resid 660 through 663 and (name N or name CA or name C or \ name O or name CB )) or resid 664 through 862 or resid 901 or resid 902)) selection = (chain 'D' and (resid 48 through 278 or resid 298 through 339 or resid 344 throu \ gh 351 or (resid 352 through 353 and (name N or name CA or name C or name O or n \ ame CB )) or resid 354 through 477 or resid 480 through 681 or resid 690 through \ 829 or resid 846 through 862 or resid 901 or resid 902)) } 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 individual isotropic 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: 5.170 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: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 47.340 Find NCS groups from input model: 1.250 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 : 0.003 0.037 22403 Z= 0.130 Angle : 0.560 9.424 30412 Z= 0.287 Chirality : 0.044 0.431 3430 Planarity : 0.004 0.057 3918 Dihedral : 14.282 88.250 8151 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.50 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2784 helix: -0.64 (0.17), residues: 890 sheet: -0.68 (0.27), residues: 401 loop : -1.38 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 315 HIS 0.005 0.001 HIS B 346 PHE 0.019 0.001 PHE B 161 TYR 0.019 0.001 TYR C 261 ARG 0.007 0.000 ARG A 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 6) link_NAG-ASN : angle 4.15940 ( 18) hydrogen bonds : bond 0.31092 ( 662) hydrogen bonds : angle 8.48114 ( 1836) SS BOND : bond 0.00228 ( 13) SS BOND : angle 0.81694 ( 26) covalent geometry : bond 0.00299 (22384) covalent geometry : angle 0.55116 (30368) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 2.265 Fit side-chains REVERT: A 43 ARG cc_start: 0.8505 (mtp85) cc_final: 0.8248 (mmm-85) REVERT: B 265 LEU cc_start: 0.7332 (mp) cc_final: 0.6529 (tt) REVERT: C 74 MET cc_start: 0.8419 (tpt) cc_final: 0.8122 (tpp) REVERT: C 290 GLN cc_start: 0.7125 (tm-30) cc_final: 0.6807 (tm-30) REVERT: C 643 ILE cc_start: 0.8452 (pt) cc_final: 0.8223 (pt) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3695 time to fit residues: 139.4390 Evaluate side-chains 205 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 4.9990 chunk 213 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 73 optimal weight: 40.0000 chunk 144 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 164 optimal weight: 0.0980 chunk 256 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.124546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090626 restraints weight = 65773.908| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.01 r_work: 0.3267 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22403 Z= 0.164 Angle : 0.611 8.065 30412 Z= 0.320 Chirality : 0.046 0.325 3430 Planarity : 0.005 0.052 3918 Dihedral : 4.987 58.276 3191 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 0.62 % Allowed : 8.14 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2784 helix: -0.37 (0.17), residues: 963 sheet: -0.78 (0.27), residues: 398 loop : -1.60 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 315 HIS 0.006 0.001 HIS C 780 PHE 0.045 0.002 PHE B 669 TYR 0.032 0.001 TYR C 261 ARG 0.006 0.000 ARG B 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 6) link_NAG-ASN : angle 3.03155 ( 18) hydrogen bonds : bond 0.05235 ( 662) hydrogen bonds : angle 5.97068 ( 1836) SS BOND : bond 0.00278 ( 13) SS BOND : angle 0.91007 ( 26) covalent geometry : bond 0.00385 (22384) covalent geometry : angle 0.60681 (30368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 2.211 Fit side-chains REVERT: A 751 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7348 (pm20) REVERT: C 290 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7263 (tm-30) REVERT: D 224 ASP cc_start: 0.8145 (p0) cc_final: 0.7914 (p0) REVERT: D 404 TRP cc_start: 0.7570 (t-100) cc_final: 0.7125 (t-100) REVERT: D 440 ARG cc_start: 0.8485 (tpm170) cc_final: 0.8271 (tpm170) outliers start: 14 outliers final: 8 residues processed: 227 average time/residue: 0.3396 time to fit residues: 122.0749 Evaluate side-chains 214 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 206 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 369 TRP Chi-restraints excluded: chain D residue 499 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 49 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 4 optimal weight: 30.0000 chunk 158 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 293 HIS ** 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 = 0.4170 r_free = 0.4170 target = 0.121352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.088684 restraints weight = 66471.473| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.35 r_work: 0.3285 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22403 Z= 0.123 Angle : 0.555 8.380 30412 Z= 0.286 Chirality : 0.044 0.307 3430 Planarity : 0.004 0.043 3918 Dihedral : 4.734 59.818 3191 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 1.19 % Allowed : 11.92 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.16), residues: 2784 helix: -0.08 (0.17), residues: 970 sheet: -0.66 (0.28), residues: 388 loop : -1.69 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 315 HIS 0.010 0.001 HIS C 101 PHE 0.028 0.001 PHE B 669 TYR 0.027 0.001 TYR C 261 ARG 0.005 0.000 ARG A 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 6) link_NAG-ASN : angle 2.85642 ( 18) hydrogen bonds : bond 0.04203 ( 662) hydrogen bonds : angle 5.29116 ( 1836) SS BOND : bond 0.00264 ( 13) SS BOND : angle 0.71123 ( 26) covalent geometry : bond 0.00285 (22384) covalent geometry : angle 0.55044 (30368) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 2.370 Fit side-chains REVERT: A 41 MET cc_start: 0.8480 (mpp) cc_final: 0.7469 (tpt) REVERT: A 127 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7917 (mp) REVERT: A 315 TRP cc_start: 0.6570 (p-90) cc_final: 0.5860 (p-90) REVERT: A 735 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.6755 (p) REVERT: A 796 GLN cc_start: 0.5808 (pp30) cc_final: 0.5441 (pp30) REVERT: B 265 LEU cc_start: 0.7171 (mp) cc_final: 0.6288 (tt) REVERT: B 658 MET cc_start: 0.8007 (ppp) cc_final: 0.7593 (ppp) REVERT: B 820 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: C 290 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7241 (tm-30) REVERT: C 780 HIS cc_start: 0.9129 (OUTLIER) cc_final: 0.7895 (m-70) REVERT: D 224 ASP cc_start: 0.8155 (p0) cc_final: 0.7852 (p0) REVERT: D 440 ARG cc_start: 0.8507 (tpm170) cc_final: 0.8230 (tpm170) outliers start: 27 outliers final: 12 residues processed: 229 average time/residue: 0.3013 time to fit residues: 111.2423 Evaluate side-chains 215 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 820 GLU Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 369 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 96 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 140 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 166 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 279 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS C 162 HIS ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.118935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.088925 restraints weight = 66558.751| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.35 r_work: 0.3208 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 22403 Z= 0.327 Angle : 0.707 9.625 30412 Z= 0.367 Chirality : 0.051 0.352 3430 Planarity : 0.005 0.050 3918 Dihedral : 5.332 54.569 3191 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.05 % Favored : 91.81 % Rotamer: Outliers : 1.63 % Allowed : 14.69 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2784 helix: -0.27 (0.17), residues: 980 sheet: -1.03 (0.27), residues: 391 loop : -1.79 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 315 HIS 0.013 0.002 HIS A 404 PHE 0.044 0.003 PHE A 458 TYR 0.022 0.002 TYR A 410 ARG 0.004 0.000 ARG C 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 6) link_NAG-ASN : angle 3.77331 ( 18) hydrogen bonds : bond 0.04932 ( 662) hydrogen bonds : angle 5.42027 ( 1836) SS BOND : bond 0.00499 ( 13) SS BOND : angle 1.18817 ( 26) covalent geometry : bond 0.00826 (22384) covalent geometry : angle 0.70049 (30368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 2.476 Fit side-chains REVERT: A 127 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7957 (mp) REVERT: A 160 TRP cc_start: 0.7652 (m-10) cc_final: 0.6790 (m-10) REVERT: A 315 TRP cc_start: 0.6807 (p-90) cc_final: 0.6064 (p-90) REVERT: A 400 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.7230 (tt) REVERT: B 658 MET cc_start: 0.7954 (ppp) cc_final: 0.7532 (ppp) REVERT: C 275 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7739 (mmmm) REVERT: C 290 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7470 (tm-30) REVERT: C 533 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: C 777 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8310 (mp) REVERT: D 384 ASN cc_start: 0.8238 (p0) cc_final: 0.6963 (p0) REVERT: D 440 ARG cc_start: 0.8527 (tpm170) cc_final: 0.8279 (tpm170) outliers start: 37 outliers final: 21 residues processed: 239 average time/residue: 0.3131 time to fit residues: 120.4015 Evaluate side-chains 231 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 777 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 369 TRP Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 517 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 202 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 271 optimal weight: 0.0010 chunk 254 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 HIS C 101 HIS ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.120787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.089079 restraints weight = 66581.796| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.56 r_work: 0.3242 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22403 Z= 0.109 Angle : 0.552 8.291 30412 Z= 0.284 Chirality : 0.044 0.324 3430 Planarity : 0.004 0.048 3918 Dihedral : 4.781 58.180 3191 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 1.72 % Allowed : 15.79 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.16), residues: 2784 helix: 0.09 (0.17), residues: 969 sheet: -0.96 (0.26), residues: 411 loop : -1.74 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 315 HIS 0.008 0.001 HIS C 101 PHE 0.020 0.001 PHE C 458 TYR 0.021 0.001 TYR C 261 ARG 0.005 0.000 ARG D 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 6) link_NAG-ASN : angle 3.44153 ( 18) hydrogen bonds : bond 0.03339 ( 662) hydrogen bonds : angle 5.00554 ( 1836) SS BOND : bond 0.00243 ( 13) SS BOND : angle 0.66588 ( 26) covalent geometry : bond 0.00247 (22384) covalent geometry : angle 0.54590 (30368) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 2.412 Fit side-chains REVERT: A 160 TRP cc_start: 0.7593 (m-10) cc_final: 0.7145 (m-10) REVERT: A 315 TRP cc_start: 0.6611 (p-90) cc_final: 0.5891 (p-90) REVERT: A 400 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7105 (tt) REVERT: A 796 GLN cc_start: 0.5952 (pp30) cc_final: 0.5697 (pp30) REVERT: B 265 LEU cc_start: 0.7622 (mp) cc_final: 0.6547 (tt) REVERT: B 556 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7123 (m-80) REVERT: B 658 MET cc_start: 0.8053 (ppp) cc_final: 0.7628 (ppp) REVERT: C 33 LEU cc_start: 0.6744 (mm) cc_final: 0.6463 (mt) REVERT: C 275 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7653 (mmmm) REVERT: C 354 MET cc_start: 0.7822 (ttt) cc_final: 0.7413 (mtp) REVERT: D 384 ASN cc_start: 0.8169 (p0) cc_final: 0.6949 (p0) REVERT: D 440 ARG cc_start: 0.8501 (tpm170) cc_final: 0.8218 (tpm170) outliers start: 39 outliers final: 19 residues processed: 237 average time/residue: 0.3004 time to fit residues: 115.5919 Evaluate side-chains 225 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 369 TRP Chi-restraints excluded: chain D residue 499 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 201 optimal weight: 0.5980 chunk 250 optimal weight: 0.8980 chunk 246 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 187 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 44 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 293 HIS ** 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 = 0.4171 r_free = 0.4171 target = 0.121469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.090473 restraints weight = 66562.104| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.15 r_work: 0.3264 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22403 Z= 0.112 Angle : 0.540 8.156 30412 Z= 0.278 Chirality : 0.044 0.293 3430 Planarity : 0.004 0.070 3918 Dihedral : 4.641 57.761 3191 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.57 % Favored : 93.32 % Rotamer: Outliers : 1.45 % Allowed : 16.53 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2784 helix: 0.17 (0.17), residues: 975 sheet: -0.95 (0.26), residues: 411 loop : -1.70 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 184 HIS 0.007 0.001 HIS C 101 PHE 0.042 0.001 PHE B 669 TYR 0.020 0.001 TYR C 261 ARG 0.003 0.000 ARG A 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 6) link_NAG-ASN : angle 3.24992 ( 18) hydrogen bonds : bond 0.03210 ( 662) hydrogen bonds : angle 4.84805 ( 1836) SS BOND : bond 0.00225 ( 13) SS BOND : angle 0.65824 ( 26) covalent geometry : bond 0.00263 (22384) covalent geometry : angle 0.53436 (30368) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 2.299 Fit side-chains REVERT: A 160 TRP cc_start: 0.7574 (m-10) cc_final: 0.7166 (m-10) REVERT: A 315 TRP cc_start: 0.6609 (p-90) cc_final: 0.5991 (p-90) REVERT: A 400 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7111 (tt) REVERT: A 464 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7546 (mt) REVERT: A 796 GLN cc_start: 0.5954 (pp30) cc_final: 0.5578 (pp30) REVERT: B 265 LEU cc_start: 0.7596 (mp) cc_final: 0.6497 (tt) REVERT: B 658 MET cc_start: 0.7968 (ppp) cc_final: 0.7558 (ppp) REVERT: C 33 LEU cc_start: 0.6788 (mm) cc_final: 0.6472 (mt) REVERT: C 354 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7300 (mtp) REVERT: C 398 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8231 (pp) REVERT: C 533 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: D 384 ASN cc_start: 0.8111 (p0) cc_final: 0.6889 (p0) REVERT: D 440 ARG cc_start: 0.8455 (tpm170) cc_final: 0.8155 (tpm170) outliers start: 33 outliers final: 18 residues processed: 233 average time/residue: 0.3055 time to fit residues: 115.7888 Evaluate side-chains 224 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 369 TRP Chi-restraints excluded: chain D residue 499 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 164 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 134 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.120682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089390 restraints weight = 66284.755| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.40 r_work: 0.3246 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22403 Z= 0.170 Angle : 0.582 9.023 30412 Z= 0.300 Chirality : 0.045 0.309 3430 Planarity : 0.004 0.063 3918 Dihedral : 4.775 59.448 3191 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.11 % Favored : 92.82 % Rotamer: Outliers : 1.54 % Allowed : 17.33 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.16), residues: 2784 helix: 0.15 (0.17), residues: 974 sheet: -1.00 (0.26), residues: 404 loop : -1.69 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 184 HIS 0.007 0.001 HIS C 101 PHE 0.027 0.002 PHE A 458 TYR 0.020 0.001 TYR C 261 ARG 0.006 0.000 ARG B 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 6) link_NAG-ASN : angle 3.39270 ( 18) hydrogen bonds : bond 0.03523 ( 662) hydrogen bonds : angle 4.87408 ( 1836) SS BOND : bond 0.00354 ( 13) SS BOND : angle 0.86668 ( 26) covalent geometry : bond 0.00423 (22384) covalent geometry : angle 0.57554 (30368) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 2.832 Fit side-chains REVERT: A 400 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7198 (tt) REVERT: A 464 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7622 (mt) REVERT: A 796 GLN cc_start: 0.6007 (pp30) cc_final: 0.5591 (pp30) REVERT: B 265 LEU cc_start: 0.7651 (mp) cc_final: 0.6596 (tt) REVERT: B 556 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: B 658 MET cc_start: 0.8005 (ppp) cc_final: 0.7589 (ppp) REVERT: C 33 LEU cc_start: 0.6839 (mm) cc_final: 0.6550 (mt) REVERT: C 398 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8295 (pp) REVERT: C 533 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: D 384 ASN cc_start: 0.8157 (p0) cc_final: 0.6962 (p0) REVERT: D 440 ARG cc_start: 0.8480 (tpm170) cc_final: 0.8205 (tpm170) outliers start: 35 outliers final: 22 residues processed: 229 average time/residue: 0.3535 time to fit residues: 132.9706 Evaluate side-chains 232 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 820 GLU Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 369 TRP Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 757 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 216 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 224 optimal weight: 0.1980 chunk 231 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.121592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.090691 restraints weight = 66569.424| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.46 r_work: 0.3251 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22403 Z= 0.101 Angle : 0.538 10.697 30412 Z= 0.275 Chirality : 0.043 0.282 3430 Planarity : 0.004 0.058 3918 Dihedral : 4.527 56.149 3191 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.32 % Favored : 93.61 % Rotamer: Outliers : 1.32 % Allowed : 17.77 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2784 helix: 0.30 (0.17), residues: 974 sheet: -0.79 (0.27), residues: 402 loop : -1.70 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 272 HIS 0.007 0.001 HIS C 101 PHE 0.046 0.001 PHE B 669 TYR 0.020 0.001 TYR C 261 ARG 0.002 0.000 ARG A 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 6) link_NAG-ASN : angle 3.21188 ( 18) hydrogen bonds : bond 0.02930 ( 662) hydrogen bonds : angle 4.71251 ( 1836) SS BOND : bond 0.00264 ( 13) SS BOND : angle 0.61366 ( 26) covalent geometry : bond 0.00231 (22384) covalent geometry : angle 0.53222 (30368) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 2.446 Fit side-chains REVERT: A 41 MET cc_start: 0.8075 (mpp) cc_final: 0.7491 (tpt) REVERT: A 400 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7143 (tt) REVERT: A 464 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7529 (mt) REVERT: A 735 VAL cc_start: 0.7544 (OUTLIER) cc_final: 0.6338 (t) REVERT: A 796 GLN cc_start: 0.6024 (pp30) cc_final: 0.5594 (pp30) REVERT: B 265 LEU cc_start: 0.7610 (mp) cc_final: 0.6561 (tt) REVERT: B 658 MET cc_start: 0.7983 (ppp) cc_final: 0.7561 (ppp) REVERT: C 33 LEU cc_start: 0.6750 (mm) cc_final: 0.6436 (mt) REVERT: C 354 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7350 (mtp) REVERT: C 398 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8307 (pp) REVERT: C 533 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7112 (m-80) REVERT: D 384 ASN cc_start: 0.8093 (p0) cc_final: 0.6884 (p0) REVERT: D 440 ARG cc_start: 0.8516 (tpm170) cc_final: 0.8223 (tpm170) outliers start: 30 outliers final: 19 residues processed: 223 average time/residue: 0.2982 time to fit residues: 108.8485 Evaluate side-chains 230 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 734 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 104 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 190 optimal weight: 0.0670 chunk 223 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 184 optimal weight: 0.0970 chunk 135 optimal weight: 2.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 134 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.122320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.093922 restraints weight = 66631.093| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.66 r_work: 0.3270 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22403 Z= 0.095 Angle : 0.523 8.335 30412 Z= 0.267 Chirality : 0.043 0.254 3430 Planarity : 0.004 0.052 3918 Dihedral : 4.335 55.571 3191 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % Rotamer: Outliers : 1.23 % Allowed : 18.29 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.14 (0.16), residues: 2784 helix: 0.46 (0.17), residues: 975 sheet: -0.71 (0.27), residues: 394 loop : -1.67 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 272 HIS 0.008 0.001 HIS C 101 PHE 0.026 0.001 PHE B 161 TYR 0.021 0.001 TYR C 261 ARG 0.002 0.000 ARG A 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 6) link_NAG-ASN : angle 2.94154 ( 18) hydrogen bonds : bond 0.02675 ( 662) hydrogen bonds : angle 4.57061 ( 1836) SS BOND : bond 0.00248 ( 13) SS BOND : angle 0.58465 ( 26) covalent geometry : bond 0.00213 (22384) covalent geometry : angle 0.51808 (30368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 2.364 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.8085 (mpp) cc_final: 0.7492 (tpt) REVERT: A 400 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7104 (tt) REVERT: A 464 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7554 (mt) REVERT: A 735 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.6349 (t) REVERT: A 796 GLN cc_start: 0.5968 (pp30) cc_final: 0.5542 (pp30) REVERT: B 265 LEU cc_start: 0.7618 (mp) cc_final: 0.6578 (tt) REVERT: B 658 MET cc_start: 0.7874 (ppp) cc_final: 0.7464 (ppp) REVERT: C 33 LEU cc_start: 0.6732 (mm) cc_final: 0.6418 (mt) REVERT: C 354 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7372 (mtp) REVERT: C 502 MET cc_start: 0.8501 (mmm) cc_final: 0.8290 (mmm) REVERT: C 533 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: D 243 ILE cc_start: 0.8398 (mm) cc_final: 0.8169 (mm) REVERT: D 384 ASN cc_start: 0.8047 (p0) cc_final: 0.6837 (p0) REVERT: D 440 ARG cc_start: 0.8505 (tpm170) cc_final: 0.8215 (tpm170) outliers start: 28 outliers final: 20 residues processed: 221 average time/residue: 0.3068 time to fit residues: 110.3183 Evaluate side-chains 227 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 734 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 43 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 212 optimal weight: 0.9980 chunk 199 optimal weight: 0.0980 chunk 228 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.121298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.089814 restraints weight = 67057.124| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.32 r_work: 0.3277 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22403 Z= 0.140 Angle : 0.554 8.440 30412 Z= 0.283 Chirality : 0.044 0.274 3430 Planarity : 0.004 0.053 3918 Dihedral : 4.504 58.294 3191 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.72 % Favored : 93.21 % Rotamer: Outliers : 1.32 % Allowed : 18.12 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.23 (0.16), residues: 2784 helix: 0.40 (0.17), residues: 973 sheet: -0.87 (0.26), residues: 416 loop : -1.69 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 272 HIS 0.007 0.001 HIS C 101 PHE 0.048 0.002 PHE B 669 TYR 0.021 0.001 TYR C 261 ARG 0.004 0.000 ARG D 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 6) link_NAG-ASN : angle 3.11568 ( 18) hydrogen bonds : bond 0.03133 ( 662) hydrogen bonds : angle 4.61881 ( 1836) SS BOND : bond 0.00275 ( 13) SS BOND : angle 0.74308 ( 26) covalent geometry : bond 0.00343 (22384) covalent geometry : angle 0.54889 (30368) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 2.389 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.8088 (mpp) cc_final: 0.7500 (tpt) REVERT: A 400 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7166 (tt) REVERT: A 464 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7576 (mt) REVERT: B 265 LEU cc_start: 0.7607 (mp) cc_final: 0.6501 (tt) REVERT: B 556 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: B 658 MET cc_start: 0.7856 (ppp) cc_final: 0.7463 (ppp) REVERT: C 33 LEU cc_start: 0.6820 (mm) cc_final: 0.6503 (mt) REVERT: C 209 MET cc_start: 0.8703 (mmm) cc_final: 0.8443 (tpp) REVERT: C 354 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7309 (mtp) REVERT: C 502 MET cc_start: 0.8521 (mmm) cc_final: 0.8315 (mmm) REVERT: C 533 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: D 243 ILE cc_start: 0.8409 (mm) cc_final: 0.8123 (mm) REVERT: D 384 ASN cc_start: 0.8128 (p0) cc_final: 0.6923 (p0) REVERT: D 440 ARG cc_start: 0.8522 (tpm170) cc_final: 0.8201 (tpm170) outliers start: 30 outliers final: 22 residues processed: 221 average time/residue: 0.2971 time to fit residues: 107.1954 Evaluate side-chains 227 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 734 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 62 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 101 optimal weight: 0.0030 chunk 277 optimal weight: 0.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.121266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.090808 restraints weight = 66563.143| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.10 r_work: 0.3288 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22403 Z= 0.127 Angle : 0.555 15.078 30412 Z= 0.282 Chirality : 0.044 0.281 3430 Planarity : 0.004 0.052 3918 Dihedral : 4.487 57.674 3191 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.35 % Rotamer: Outliers : 1.19 % Allowed : 18.38 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.16), residues: 2784 helix: 0.41 (0.17), residues: 973 sheet: -0.86 (0.26), residues: 416 loop : -1.71 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 498 HIS 0.012 0.001 HIS D 197 PHE 0.032 0.002 PHE B 161 TYR 0.021 0.001 TYR C 261 ARG 0.003 0.000 ARG A 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 6) link_NAG-ASN : angle 3.14186 ( 18) hydrogen bonds : bond 0.03028 ( 662) hydrogen bonds : angle 4.62260 ( 1836) SS BOND : bond 0.00255 ( 13) SS BOND : angle 0.69123 ( 26) covalent geometry : bond 0.00310 (22384) covalent geometry : angle 0.55016 (30368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11399.94 seconds wall clock time: 198 minutes 2.67 seconds (11882.67 seconds total)