Starting phenix.real_space_refine on Fri May 23 17:24:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d39_46528/05_2025/9d39_46528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d39_46528/05_2025/9d39_46528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d39_46528/05_2025/9d39_46528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d39_46528/05_2025/9d39_46528.map" model { file = "/net/cci-nas-00/data/ceres_data/9d39_46528/05_2025/9d39_46528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d39_46528/05_2025/9d39_46528.cif" } resolution = 3.65 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= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 82 atoms to isotropic. 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 134 5.16 5 C 15562 2.51 5 N 4091 2.21 5 O 4488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24275 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6196 Classifications: {'peptide': 794} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 35, 'TRANS': 758} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 5852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5852 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 28, 'TRANS': 746} Chain breaks: 3 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 183 Chain: "C" Number of atoms: 6235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6235 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 35, 'TRANS': 763} Chain breaks: 2 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "D" Number of atoms: 5884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 5884 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 728} Chain breaks: 4 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Classifications: {'peptide': 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: 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Classifications: {'peptide': 1} Time building chain proxies: 14.69, per 1000 atoms: 0.61 Number of scatterers: 24275 At special positions: 0 Unit cell: (118.261, 142.244, 181.94, 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 134 16.00 O 4488 8.00 N 4091 7.00 C 15562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, 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 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " 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 C 744 " - pdb=" SG CYS C 798 " 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 A 903 " - " ASN A 471 " " NAG C 902 " - " ASN C 771 " Time building additional restraints: 5.94 Conformation dependent library (CDL) restraints added in 3.2 seconds 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 2JL B 901 " pdb=" CB 2JL D 901 " Number of C-beta restraints generated: 5834 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 33 sheets defined 41.7% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.642A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 4.261A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 Processing helix chain 'A' and resid 103 through 111 removed outlier: 4.538A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.817A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.546A pdb=" N ARG A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 206 removed outlier: 3.980A pdb=" N ALA A 206 " --> pdb=" O ASN A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 206' Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.477A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.979A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.758A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.579A pdb=" N ILE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 325 through 328 removed outlier: 3.885A pdb=" N SER A 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.518A pdb=" N THR A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 522 through 526 Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.711A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 removed outlier: 3.563A pdb=" N TRP A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 657 removed outlier: 3.732A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 removed outlier: 4.190A pdb=" N ASN A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 4.144A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.608A pdb=" N TYR A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.711A pdb=" N ALA A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.620A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 removed outlier: 3.679A pdb=" N HIS A 780 " --> pdb=" O ILE A 776 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 793 removed outlier: 4.255A pdb=" N ASP A 789 " --> pdb=" O MET A 785 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 790 " --> pdb=" O GLU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 837 removed outlier: 3.616A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.561A pdb=" N ILE B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 removed outlier: 3.603A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.545A pdb=" N PHE B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 165 removed outlier: 3.731A pdb=" N MET B 157 " --> pdb=" O GLN B 153 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.734A pdb=" N ASN B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.630A pdb=" N GLN B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLN B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.532A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.526A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 312 removed outlier: 3.542A pdb=" N ALA B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.833A pdb=" N ASN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 555 through 576 removed outlier: 3.896A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.672A pdb=" N GLY B 611 " --> pdb=" O TRP B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 654 removed outlier: 3.532A pdb=" N PHE B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.758A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.786A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.786A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.315A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 779 " --> pdb=" O GLN B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 797 Processing helix chain 'B' and resid 819 through 838 removed outlier: 3.798A pdb=" N LEU B 833 " --> pdb=" O MET B 829 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.773A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.886A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 76' Processing helix chain 'C' and resid 77 through 82 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 115 removed outlier: 3.828A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 157 removed outlier: 4.023A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET C 155 " --> pdb=" O TRP C 151 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 182 removed outlier: 4.613A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU C 181 " --> pdb=" O GLN C 177 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 210 removed outlier: 3.872A pdb=" N MET C 209 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 205 through 210' Processing helix chain 'C' and resid 224 through 235 removed outlier: 3.531A pdb=" N ARG C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 4.210A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.605A pdb=" N VAL C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 removed outlier: 3.516A pdb=" N PHE C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.716A pdb=" N THR C 419 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 removed outlier: 3.941A pdb=" N LEU C 463 " --> pdb=" O CYS C 459 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.750A pdb=" N GLY C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 562 through 580 removed outlier: 3.836A pdb=" N LEU C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 615 removed outlier: 3.756A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 658 removed outlier: 3.689A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA C 637 " --> pdb=" O GLY C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 668 removed outlier: 4.063A pdb=" N ASN C 668 " --> pdb=" O THR C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 665 through 668' Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 693 Processing helix chain 'C' and resid 696 through 698 No H-bonds generated for 'chain 'C' and resid 696 through 698' Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.783A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 4.291A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 783 removed outlier: 4.492A pdb=" N ASN C 771 " --> pdb=" O PRO C 767 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY C 783 " --> pdb=" O SER C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 792 removed outlier: 4.040A pdb=" N ASP C 789 " --> pdb=" O MET C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 836 removed outlier: 5.337A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 825 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 64 through 75 removed outlier: 4.409A pdb=" N ARG D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Proline residue: D 71 - end of helix removed outlier: 3.507A pdb=" N ALA D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 110 removed outlier: 3.733A pdb=" N GLN D 102 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS D 104 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 4.405A pdb=" N ILE D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 182 removed outlier: 3.622A pdb=" N GLU D 177 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 180 " --> pdb=" O PHE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 removed outlier: 4.011A pdb=" N ILE D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 249 through 263 removed outlier: 4.498A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Proline residue: D 255 - end of helix removed outlier: 3.745A pdb=" N GLU D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 338 removed outlier: 4.024A pdb=" N VAL D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA D 333 " --> pdb=" O ARG D 329 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 500 Processing helix chain 'D' and resid 523 through 530 removed outlier: 3.674A pdb=" N VAL D 528 " --> pdb=" O MET D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 548 removed outlier: 3.649A pdb=" N GLU D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 606 removed outlier: 3.557A pdb=" N PHE D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR D 606 " --> pdb=" O PHE D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 641 removed outlier: 3.802A pdb=" N LYS D 631 " --> pdb=" O PHE D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 681 removed outlier: 3.794A pdb=" N MET D 681 " --> pdb=" O LEU D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 700 Processing helix chain 'D' and resid 716 through 726 removed outlier: 3.653A pdb=" N TYR D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 734 removed outlier: 3.645A pdb=" N VAL D 734 " --> pdb=" O HIS D 730 " (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 Processing helix chain 'D' and resid 759 through 769 removed outlier: 4.297A pdb=" N TYR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET D 766 " --> pdb=" O VAL D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 773 Processing helix chain 'D' and resid 799 through 813 Processing helix chain 'D' and resid 814 through 822 removed outlier: 3.822A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 819 " --> pdb=" O GLU D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 844 No H-bonds generated for 'chain 'D' and resid 842 through 844' Processing helix chain 'D' and resid 845 through 872 removed outlier: 3.813A pdb=" N PHE D 849 " --> pdb=" O MET D 845 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 852 " --> pdb=" O VAL D 848 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TYR D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TRP D 871 " --> pdb=" O HIS D 867 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 64 removed outlier: 5.640A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR A 88 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 197 removed outlier: 8.209A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.612A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.525A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.618A pdb=" N THR A 402 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AA8, first strand: chain 'A' and resid 485 through 488 removed outlier: 3.558A pdb=" N THR A 486 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.114A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 38 through 41 removed outlier: 5.944A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 204 removed outlier: 7.182A pdb=" N PHE B 169 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU B 201 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE B 171 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE B 168 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU B 229 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB4, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB5, first strand: chain 'B' and resid 455 through 457 removed outlier: 7.353A pdb=" N LEU B 480 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLN B 437 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 508 through 514 removed outlier: 4.824A pdb=" N GLY B 511 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY B 763 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 683 through 684 removed outlier: 5.686A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 32 removed outlier: 7.028A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 196 through 197 removed outlier: 7.302A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AC2, first strand: chain 'C' and resid 366 through 367 Processing sheet with id=AC3, first strand: chain 'C' and resid 397 through 402 removed outlier: 7.284A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 410 through 413 Processing sheet with id=AC5, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC6, first strand: chain 'C' and resid 512 through 513 Processing sheet with id=AC7, first strand: chain 'C' and resid 730 through 732 removed outlier: 3.812A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.644A pdb=" N LEU D 55 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 116 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL D 115 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL D 144 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE D 117 " --> pdb=" O VAL D 144 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 188 through 191 removed outlier: 3.618A pdb=" N PHE D 305 " --> pdb=" O TRP D 272 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU D 387 " --> pdb=" O SER D 403 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER D 403 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL D 389 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER D 391 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU D 399 " --> pdb=" O SER D 391 " (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 431 through 436 removed outlier: 7.362A pdb=" N LEU D 432 " --> pdb=" O ASP D 504 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N TYR D 506 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL D 434 " --> pdb=" O TYR D 506 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 443 through 446 removed outlier: 3.941A pdb=" N CYS D 483 " --> pdb=" O GLU D 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 515 through 516 Processing sheet with id=AD5, first strand: chain 'D' and resid 564 through 566 Processing sheet with id=AD6, first strand: chain 'D' and resid 710 through 711 836 hydrogen bonds defined for protein. 2418 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: 9.21 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3978 1.31 - 1.44: 6670 1.44 - 1.57: 13945 1.57 - 1.69: 0 1.69 - 1.82: 229 Bond restraints: 24822 Sorted by residual: bond pdb=" CAT 2JL B 901 " pdb=" NAZ 2JL B 901 " ideal model delta sigma weight residual 1.339 1.485 -0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" CAT 2JL D 901 " pdb=" NAZ 2JL D 901 " ideal model delta sigma weight residual 1.339 1.482 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" CAT 2JL B 901 " pdb=" CAU 2JL B 901 " ideal model delta sigma weight residual 1.496 1.563 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" CAT 2JL D 901 " pdb=" CAU 2JL D 901 " ideal model delta sigma weight residual 1.496 1.560 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" CAW 2JL D 901 " pdb=" CAY 2JL D 901 " ideal model delta sigma weight residual 1.413 1.367 0.046 2.00e-02 2.50e+03 5.37e+00 ... (remaining 24817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 33223 2.02 - 4.04: 404 4.04 - 6.06: 77 6.06 - 8.08: 14 8.08 - 10.10: 6 Bond angle restraints: 33724 Sorted by residual: angle pdb=" CA LYS B 473 " pdb=" CB LYS B 473 " pdb=" CG LYS B 473 " ideal model delta sigma weight residual 114.10 123.13 -9.03 2.00e+00 2.50e-01 2.04e+01 angle pdb=" CB MET D 836 " pdb=" CG MET D 836 " pdb=" SD MET D 836 " ideal model delta sigma weight residual 112.70 122.80 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CB LYS B 473 " pdb=" CG LYS B 473 " pdb=" CD LYS B 473 " ideal model delta sigma weight residual 111.30 118.90 -7.60 2.30e+00 1.89e-01 1.09e+01 angle pdb=" CA LYS D 481 " pdb=" CB LYS D 481 " pdb=" CG LYS D 481 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" N VAL C 46 " pdb=" CA VAL C 46 " pdb=" C VAL C 46 " ideal model delta sigma weight residual 113.53 110.43 3.10 9.80e-01 1.04e+00 1.00e+01 ... (remaining 33719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 13050 21.50 - 43.00: 1457 43.00 - 64.50: 241 64.50 - 86.00: 47 86.00 - 107.50: 17 Dihedral angle restraints: 14812 sinusoidal: 5761 harmonic: 9051 Sorted by residual: dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 455 " pdb=" CB CYS A 455 " ideal model delta sinusoidal sigma weight residual -86.00 -168.54 82.54 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 308 " pdb=" CB CYS A 308 " ideal model delta sinusoidal sigma weight residual 93.00 12.44 80.56 1 1.00e+01 1.00e-02 8.02e+01 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 -165.63 79.63 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 14809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3306 0.061 - 0.121: 502 0.121 - 0.182: 30 0.182 - 0.242: 1 0.242 - 0.303: 2 Chirality restraints: 3841 Sorted by residual: chirality pdb=" CA 2JL D 901 " pdb=" N 2JL D 901 " pdb=" C 2JL D 901 " pdb=" CB 2JL D 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.55 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA 2JL B 901 " pdb=" N 2JL B 901 " pdb=" C 2JL B 901 " pdb=" CB 2JL B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.52 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C1 NAG C 902 " pdb=" ND2 ASN C 771 " pdb=" C2 NAG C 902 " pdb=" O5 NAG C 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 3838 not shown) Planarity restraints: 4292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 473 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C LYS B 473 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS B 473 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 474 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 117 " 0.013 2.00e-02 2.50e+03 1.69e-02 5.01e+00 pdb=" CG PHE D 117 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE D 117 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE D 117 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE D 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 117 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 117 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 765 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C ASP C 765 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP C 765 " 0.014 2.00e-02 2.50e+03 pdb=" N SER C 766 " 0.012 2.00e-02 2.50e+03 ... (remaining 4289 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3637 2.76 - 3.29: 25284 3.29 - 3.83: 40986 3.83 - 4.36: 46754 4.36 - 4.90: 78697 Nonbonded interactions: 195358 Sorted by model distance: nonbonded pdb=" OG SER C 224 " pdb=" OD1 ASP C 226 " model vdw 2.219 3.040 nonbonded pdb=" O LYS B 79 " pdb=" OG1 THR B 83 " model vdw 2.224 3.040 nonbonded pdb=" O PRO C 670 " pdb=" ND2 ASN C 674 " model vdw 2.228 3.120 nonbonded pdb=" OG1 THR D 185 " pdb=" O GLY D 214 " model vdw 2.250 3.040 nonbonded pdb=" OE2 GLU C 39 " pdb=" OG1 THR C 66 " model vdw 2.259 3.040 ... (remaining 195353 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 35 or (resid 36 and (name N or name CA or name C or name \ O or name CB )) or resid 37 through 186 or (resid 187 through 188 and (name N or \ name CA or name C or name O or name CB )) or resid 189 through 392 or (resid 39 \ 3 through 394 and (name N or name CA or name C or name O or name CB )) or resid \ 395 through 416 or (resid 417 and (name N or name CA or name C or name O or name \ CB )) or resid 418 through 488 or (resid 489 and (name N or name CA or name C o \ r name O or name CB )) or resid 490 through 494 or (resid 495 and (name N or nam \ e CA or name C or name O or name CB )) or resid 496 through 624 or (resid 625 an \ d (name N or name CA or name C or name O or name CB )) or resid 626 through 837 \ or resid 903)) selection = (chain 'C' and (resid 25 through 259 or (resid 260 and (name N or name CA or nam \ e C or name O or name CB )) or resid 261 through 393 or (resid 394 and (name N o \ r name CA or name C or name O or name CB )) or resid 395 through 544 or (resid 5 \ 45 and (name N or name CA or name C or name O or name CB )) or resid 546 through \ 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or r \ esid 550 through 677 or (resid 678 and (name N or name CA or name C or name O or \ name CB )) or resid 679 through 703 or (resid 704 and (name N or name CA or nam \ e C or name O or name CB )) or resid 705 through 750 or (resid 751 and (name N o \ r name CA or name C or name O or name CB )) or resid 752 through 798 or resid 80 \ 4 through 808 or (resid 809 and (name N or name CA or name C or name O or name C \ B )) or resid 810 or (resid 811 through 812 and (name N or name CA or name C or \ name O or name CB )) or resid 813 through 831 or (resid 832 through 833 and (nam \ e N or name CA or name C or name O or name CB )) or resid 834 through 836 or (re \ sid 837 and (name N or name CA or name C or name O or name CB )) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 54.210 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 0.146 24840 Z= 0.144 Angle : 0.574 10.096 33763 Z= 0.280 Chirality : 0.043 0.303 3841 Planarity : 0.003 0.036 4289 Dihedral : 17.774 107.497 8933 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.38 % Favored : 92.49 % Rotamer: Outliers : 0.19 % Allowed : 34.13 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % 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: -1.47 (0.15), residues: 3102 helix: -0.10 (0.16), residues: 1113 sheet: -0.98 (0.30), residues: 340 loop : -1.61 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 637 HIS 0.006 0.001 HIS A 780 PHE 0.039 0.001 PHE D 117 TYR 0.013 0.001 TYR B 479 ARG 0.005 0.000 ARG A 548 Details of bonding type rmsd link_NAG-ASN : bond 0.01180 ( 3) link_NAG-ASN : angle 4.31490 ( 9) hydrogen bonds : bond 0.28334 ( 836) hydrogen bonds : angle 8.58143 ( 2418) SS BOND : bond 0.00194 ( 15) SS BOND : angle 0.98383 ( 30) covalent geometry : bond 0.00315 (24822) covalent geometry : angle 0.56957 (33724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 2.680 Fit side-chains REVERT: B 537 MET cc_start: 0.7087 (mmm) cc_final: 0.6583 (mmm) REVERT: C 166 LEU cc_start: 0.9050 (pt) cc_final: 0.8411 (tp) REVERT: C 502 MET cc_start: 0.7868 (mmt) cc_final: 0.7098 (mmt) outliers start: 5 outliers final: 1 residues processed: 183 average time/residue: 0.3111 time to fit residues: 95.7552 Evaluate side-chains 173 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 159 optimal weight: 40.0000 chunk 125 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 181 optimal weight: 30.0000 chunk 282 optimal weight: 0.0060 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 47 ASN A 59 GLN A 146 HIS A 239 ASN A 290 GLN A 293 HIS A 742 GLN B 118 GLN B 159 ASN B 359 HIS C 177 GLN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 ASN C 705 HIS C 770 GLN C 782 ASN D 351 GLN D 407 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.115189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.087402 restraints weight = 81835.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.084996 restraints weight = 56393.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.086157 restraints weight = 52963.602| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24840 Z= 0.124 Angle : 0.572 9.936 33763 Z= 0.295 Chirality : 0.044 0.211 3841 Planarity : 0.004 0.036 4289 Dihedral : 5.792 74.377 3464 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.22 % Favored : 92.65 % Rotamer: Outliers : 2.88 % Allowed : 31.87 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % 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: -1.34 (0.15), residues: 3102 helix: 0.18 (0.16), residues: 1161 sheet: -0.87 (0.31), residues: 307 loop : -1.71 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 636 HIS 0.004 0.001 HIS D 794 PHE 0.020 0.001 PHE D 117 TYR 0.015 0.001 TYR A 456 ARG 0.004 0.000 ARG C 124 Details of bonding type rmsd link_NAG-ASN : bond 0.01554 ( 3) link_NAG-ASN : angle 4.42544 ( 9) hydrogen bonds : bond 0.05676 ( 836) hydrogen bonds : angle 5.83098 ( 2418) SS BOND : bond 0.00221 ( 15) SS BOND : angle 0.89422 ( 30) covalent geometry : bond 0.00263 (24822) covalent geometry : angle 0.56670 (33724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 192 time to evaluate : 2.519 Fit side-chains REVERT: A 233 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7798 (ttm110) REVERT: A 555 MET cc_start: 0.8155 (mtp) cc_final: 0.7891 (mtp) REVERT: B 307 MET cc_start: 0.6678 (mmm) cc_final: 0.6102 (mmm) REVERT: B 537 MET cc_start: 0.6940 (mmm) cc_final: 0.5966 (mmm) REVERT: B 702 MET cc_start: 0.8375 (tpp) cc_final: 0.7974 (tpp) REVERT: B 738 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7681 (t80) REVERT: B 797 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7217 (pt) REVERT: B 829 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6905 (mtm) REVERT: C 166 LEU cc_start: 0.9073 (pt) cc_final: 0.8489 (tp) REVERT: C 178 LYS cc_start: 0.8947 (mppt) cc_final: 0.8699 (mppt) REVERT: C 354 MET cc_start: 0.7877 (mmm) cc_final: 0.7656 (mmm) REVERT: C 502 MET cc_start: 0.7824 (mmt) cc_final: 0.7597 (mmt) REVERT: D 363 TYR cc_start: 0.6368 (p90) cc_final: 0.5960 (p90) REVERT: D 588 MET cc_start: 0.7644 (tmm) cc_final: 0.7389 (tmm) outliers start: 74 outliers final: 21 residues processed: 252 average time/residue: 0.3171 time to fit residues: 133.1839 Evaluate side-chains 203 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 680 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 0.0370 chunk 107 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 298 optimal weight: 4.9990 chunk 81 optimal weight: 0.0980 chunk 240 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 284 optimal weight: 0.0470 chunk 128 optimal weight: 9.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 492 ASN A 709 HIS ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 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 = 0.4214 r_free = 0.4214 target = 0.115427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.088548 restraints weight = 81806.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.085966 restraints weight = 56075.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.086856 restraints weight = 55069.837| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24840 Z= 0.109 Angle : 0.549 12.716 33763 Z= 0.278 Chirality : 0.043 0.222 3841 Planarity : 0.003 0.037 4289 Dihedral : 4.496 42.681 3463 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.09 % Favored : 92.78 % Rotamer: Outliers : 3.93 % Allowed : 29.92 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % 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: -1.25 (0.15), residues: 3102 helix: 0.31 (0.16), residues: 1177 sheet: -0.99 (0.30), residues: 313 loop : -1.70 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 636 HIS 0.004 0.001 HIS C 727 PHE 0.027 0.001 PHE D 187 TYR 0.011 0.001 TYR B 479 ARG 0.004 0.000 ARG C 124 Details of bonding type rmsd link_NAG-ASN : bond 0.01254 ( 3) link_NAG-ASN : angle 4.44451 ( 9) hydrogen bonds : bond 0.04200 ( 836) hydrogen bonds : angle 5.28276 ( 2418) SS BOND : bond 0.00165 ( 15) SS BOND : angle 0.83403 ( 30) covalent geometry : bond 0.00239 (24822) covalent geometry : angle 0.54416 (33724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 194 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8120 (pp30) REVERT: A 233 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7656 (ttm110) REVERT: A 470 MET cc_start: 0.8575 (mmm) cc_final: 0.8336 (mmm) REVERT: A 555 MET cc_start: 0.8170 (mtp) cc_final: 0.7934 (mtp) REVERT: B 175 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: B 184 ASN cc_start: 0.8851 (m-40) cc_final: 0.8526 (m-40) REVERT: B 287 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6757 (t80) REVERT: B 307 MET cc_start: 0.6557 (mmm) cc_final: 0.5763 (mmm) REVERT: B 480 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8449 (mp) REVERT: B 649 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8113 (t0) REVERT: B 702 MET cc_start: 0.8387 (tpp) cc_final: 0.8060 (tpp) REVERT: B 738 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7689 (t80) REVERT: C 178 LYS cc_start: 0.8999 (mppt) cc_final: 0.8593 (mppt) REVERT: C 209 MET cc_start: 0.7405 (mpp) cc_final: 0.6910 (tpt) REVERT: C 392 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: C 470 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6537 (mtm) REVERT: C 520 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8140 (p0) REVERT: C 780 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.5940 (m-70) REVERT: D 363 TYR cc_start: 0.6410 (p90) cc_final: 0.6051 (p90) REVERT: D 393 THR cc_start: 0.6044 (OUTLIER) cc_final: 0.5769 (p) REVERT: D 588 MET cc_start: 0.7625 (tmm) cc_final: 0.7186 (tmm) REVERT: D 637 TRP cc_start: 0.7683 (OUTLIER) cc_final: 0.7262 (m-90) outliers start: 101 outliers final: 33 residues processed: 283 average time/residue: 0.3100 time to fit residues: 145.3435 Evaluate side-chains 227 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 360 LYS Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 637 TRP Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 215 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 56 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 492 ASN C 196 GLN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 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 = 0.4202 r_free = 0.4202 target = 0.114587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.088081 restraints weight = 82631.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.085146 restraints weight = 61220.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.086172 restraints weight = 56046.967| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24840 Z= 0.146 Angle : 0.558 9.340 33763 Z= 0.282 Chirality : 0.044 0.228 3841 Planarity : 0.003 0.037 4289 Dihedral : 4.236 45.952 3463 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.58 % Favored : 92.30 % Rotamer: Outliers : 4.40 % Allowed : 29.84 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 3102 helix: 0.38 (0.16), residues: 1179 sheet: -0.99 (0.30), residues: 316 loop : -1.72 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 160 HIS 0.008 0.001 HIS A 780 PHE 0.025 0.001 PHE C 458 TYR 0.021 0.001 TYR A 456 ARG 0.004 0.000 ARG B 712 Details of bonding type rmsd link_NAG-ASN : bond 0.01060 ( 3) link_NAG-ASN : angle 4.35102 ( 9) hydrogen bonds : bond 0.03869 ( 836) hydrogen bonds : angle 5.15733 ( 2418) SS BOND : bond 0.00237 ( 15) SS BOND : angle 0.90994 ( 30) covalent geometry : bond 0.00338 (24822) covalent geometry : angle 0.55349 (33724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 184 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8128 (pp30) REVERT: A 233 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7690 (ttm110) REVERT: A 237 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7691 (tmm) REVERT: A 780 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7340 (m170) REVERT: B 142 MET cc_start: 0.6697 (mmp) cc_final: 0.6428 (mmp) REVERT: B 175 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.6367 (m-80) REVERT: B 184 ASN cc_start: 0.8819 (m-40) cc_final: 0.8497 (m-40) REVERT: B 287 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6831 (t80) REVERT: B 307 MET cc_start: 0.6548 (mmm) cc_final: 0.5664 (mmm) REVERT: B 480 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8507 (mp) REVERT: B 649 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8151 (t0) REVERT: B 702 MET cc_start: 0.8482 (tpp) cc_final: 0.8185 (tpp) REVERT: B 738 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7654 (t80) REVERT: C 132 SER cc_start: 0.6815 (OUTLIER) cc_final: 0.6260 (m) REVERT: C 178 LYS cc_start: 0.9208 (mppt) cc_final: 0.8800 (mppt) REVERT: C 209 MET cc_start: 0.7549 (mpp) cc_final: 0.6893 (tpt) REVERT: C 354 MET cc_start: 0.7924 (mmm) cc_final: 0.7449 (mmm) REVERT: C 392 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.7171 (m-80) REVERT: C 470 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6583 (mtm) REVERT: C 520 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8138 (p0) REVERT: C 780 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.6157 (m-70) REVERT: C 816 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7936 (m) REVERT: D 363 TYR cc_start: 0.6417 (p90) cc_final: 0.6019 (p90) REVERT: D 393 THR cc_start: 0.5988 (OUTLIER) cc_final: 0.5701 (p) REVERT: D 588 MET cc_start: 0.7530 (tmm) cc_final: 0.7274 (tmm) REVERT: D 637 TRP cc_start: 0.7799 (OUTLIER) cc_final: 0.7349 (m-90) REVERT: D 745 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8912 (mm) outliers start: 113 outliers final: 55 residues processed: 279 average time/residue: 0.2982 time to fit residues: 138.9156 Evaluate side-chains 251 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 178 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 637 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 717 SER Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 861 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 223 optimal weight: 8.9990 chunk 259 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 227 optimal weight: 0.4980 chunk 243 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 7 optimal weight: 0.0770 chunk 58 optimal weight: 4.9990 chunk 248 optimal weight: 30.0000 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 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 = 0.4199 r_free = 0.4199 target = 0.114501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.087606 restraints weight = 82218.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.085239 restraints weight = 58273.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.086373 restraints weight = 54163.131| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24840 Z= 0.148 Angle : 0.557 9.015 33763 Z= 0.282 Chirality : 0.044 0.235 3841 Planarity : 0.003 0.055 4289 Dihedral : 4.204 49.140 3463 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.83 % Favored : 92.04 % Rotamer: Outliers : 4.40 % Allowed : 30.11 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % 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: -1.21 (0.15), residues: 3102 helix: 0.42 (0.16), residues: 1179 sheet: -1.01 (0.30), residues: 321 loop : -1.73 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 637 HIS 0.007 0.001 HIS A 780 PHE 0.023 0.001 PHE A 458 TYR 0.021 0.001 TYR A 456 ARG 0.003 0.000 ARG D 482 Details of bonding type rmsd link_NAG-ASN : bond 0.01061 ( 3) link_NAG-ASN : angle 4.22934 ( 9) hydrogen bonds : bond 0.03731 ( 836) hydrogen bonds : angle 5.08526 ( 2418) SS BOND : bond 0.00268 ( 15) SS BOND : angle 1.11719 ( 30) covalent geometry : bond 0.00343 (24822) covalent geometry : angle 0.55252 (33724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 183 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8096 (pp30) REVERT: A 233 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7638 (ttm110) REVERT: A 237 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7683 (tmm) REVERT: A 238 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8975 (tp) REVERT: A 491 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7381 (p0) REVERT: A 555 MET cc_start: 0.8211 (mtp) cc_final: 0.7997 (mtp) REVERT: A 780 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7336 (m170) REVERT: B 142 MET cc_start: 0.6897 (mmp) cc_final: 0.6583 (mmp) REVERT: B 175 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: B 184 ASN cc_start: 0.8818 (m-40) cc_final: 0.8499 (m-40) REVERT: B 287 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6867 (t80) REVERT: B 307 MET cc_start: 0.6588 (mmm) cc_final: 0.5669 (mmm) REVERT: B 480 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8555 (mp) REVERT: B 649 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8175 (t0) REVERT: B 702 MET cc_start: 0.8431 (tpp) cc_final: 0.8153 (tpp) REVERT: B 738 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7701 (t80) REVERT: C 132 SER cc_start: 0.6681 (OUTLIER) cc_final: 0.6054 (m) REVERT: C 209 MET cc_start: 0.7472 (mpp) cc_final: 0.6898 (tpt) REVERT: C 354 MET cc_start: 0.7924 (mmm) cc_final: 0.7574 (mmm) REVERT: C 392 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: C 470 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.6559 (mtm) REVERT: C 502 MET cc_start: 0.7068 (mmt) cc_final: 0.6679 (mmt) REVERT: C 520 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8155 (p0) REVERT: C 780 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.6261 (m-70) REVERT: C 816 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7950 (m) REVERT: D 393 THR cc_start: 0.6029 (OUTLIER) cc_final: 0.5751 (p) REVERT: D 637 TRP cc_start: 0.7807 (OUTLIER) cc_final: 0.7185 (m-90) REVERT: D 745 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8899 (mm) outliers start: 113 outliers final: 63 residues processed: 279 average time/residue: 0.3314 time to fit residues: 157.7986 Evaluate side-chains 260 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 177 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 360 LYS Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 TRP Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 637 TRP Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 717 SER Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 104 optimal weight: 0.6980 chunk 232 optimal weight: 0.6980 chunk 283 optimal weight: 5.9990 chunk 266 optimal weight: 20.0000 chunk 257 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 240 optimal weight: 20.0000 chunk 151 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.114653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.086950 restraints weight = 81748.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.084200 restraints weight = 55375.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.085163 restraints weight = 52333.302| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24840 Z= 0.135 Angle : 0.554 9.659 33763 Z= 0.280 Chirality : 0.043 0.236 3841 Planarity : 0.003 0.037 4289 Dihedral : 4.167 50.398 3463 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.45 % Favored : 92.42 % Rotamer: Outliers : 4.87 % Allowed : 29.72 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % 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: -1.18 (0.15), residues: 3102 helix: 0.46 (0.16), residues: 1178 sheet: -1.01 (0.30), residues: 320 loop : -1.73 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 637 HIS 0.006 0.001 HIS A 780 PHE 0.044 0.001 PHE A 583 TYR 0.019 0.001 TYR A 456 ARG 0.003 0.000 ARG C 124 Details of bonding type rmsd link_NAG-ASN : bond 0.01092 ( 3) link_NAG-ASN : angle 4.14666 ( 9) hydrogen bonds : bond 0.03555 ( 836) hydrogen bonds : angle 5.00400 ( 2418) SS BOND : bond 0.00227 ( 15) SS BOND : angle 1.02593 ( 30) covalent geometry : bond 0.00312 (24822) covalent geometry : angle 0.54950 (33724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 186 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7673 (ttm110) REVERT: A 237 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7693 (tmm) REVERT: A 491 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7314 (p0) REVERT: A 502 MET cc_start: 0.8131 (mmm) cc_final: 0.7569 (mmp) REVERT: A 780 HIS cc_start: 0.8157 (OUTLIER) cc_final: 0.7413 (m170) REVERT: B 142 MET cc_start: 0.7053 (mmp) cc_final: 0.6770 (mmp) REVERT: B 175 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6439 (m-80) REVERT: B 184 ASN cc_start: 0.8846 (m-40) cc_final: 0.8525 (m-40) REVERT: B 287 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6900 (t80) REVERT: B 307 MET cc_start: 0.6548 (mmm) cc_final: 0.5647 (mmm) REVERT: B 480 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8561 (mp) REVERT: B 649 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8190 (t0) REVERT: B 702 MET cc_start: 0.8499 (tpp) cc_final: 0.8243 (tpp) REVERT: B 738 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7650 (t80) REVERT: C 132 SER cc_start: 0.6704 (OUTLIER) cc_final: 0.6089 (m) REVERT: C 209 MET cc_start: 0.7573 (mpp) cc_final: 0.7028 (tpt) REVERT: C 392 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: C 470 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.6622 (mtm) REVERT: C 494 ASN cc_start: 0.6672 (OUTLIER) cc_final: 0.6095 (p0) REVERT: C 520 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8163 (p0) REVERT: C 780 HIS cc_start: 0.8211 (OUTLIER) cc_final: 0.6270 (m-70) REVERT: C 816 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7975 (m) REVERT: D 393 THR cc_start: 0.5954 (OUTLIER) cc_final: 0.5659 (p) REVERT: D 588 MET cc_start: 0.7621 (tmm) cc_final: 0.7419 (tmm) REVERT: D 637 TRP cc_start: 0.7849 (OUTLIER) cc_final: 0.7109 (m-90) REVERT: D 745 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8902 (mm) outliers start: 125 outliers final: 68 residues processed: 291 average time/residue: 0.3253 time to fit residues: 161.1715 Evaluate side-chains 264 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 177 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 694 ASN Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 360 LYS Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 TRP Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 637 TRP Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 717 SER Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 180 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 282 optimal weight: 0.9980 chunk 265 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.114619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.087765 restraints weight = 81969.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.084923 restraints weight = 58096.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.085788 restraints weight = 52066.158| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24840 Z= 0.132 Angle : 0.563 14.887 33763 Z= 0.282 Chirality : 0.043 0.240 3841 Planarity : 0.003 0.037 4289 Dihedral : 4.150 50.483 3463 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.54 % Favored : 92.33 % Rotamer: Outliers : 4.67 % Allowed : 29.96 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % 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: -1.18 (0.15), residues: 3102 helix: 0.47 (0.16), residues: 1184 sheet: -1.01 (0.30), residues: 320 loop : -1.75 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 637 HIS 0.006 0.001 HIS A 780 PHE 0.031 0.001 PHE A 583 TYR 0.018 0.001 TYR A 456 ARG 0.003 0.000 ARG D 482 Details of bonding type rmsd link_NAG-ASN : bond 0.01073 ( 3) link_NAG-ASN : angle 4.06623 ( 9) hydrogen bonds : bond 0.03451 ( 836) hydrogen bonds : angle 4.94766 ( 2418) SS BOND : bond 0.00204 ( 15) SS BOND : angle 1.04224 ( 30) covalent geometry : bond 0.00306 (24822) covalent geometry : angle 0.55865 (33724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 179 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8094 (pp30) REVERT: A 233 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7635 (ttm110) REVERT: A 237 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7697 (tmm) REVERT: A 238 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8980 (tp) REVERT: A 491 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7375 (p0) REVERT: A 502 MET cc_start: 0.8146 (mmm) cc_final: 0.7599 (mmp) REVERT: A 555 MET cc_start: 0.8216 (mtp) cc_final: 0.7985 (mtp) REVERT: A 702 MET cc_start: 0.7420 (pmm) cc_final: 0.7092 (pmm) REVERT: A 780 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7518 (m170) REVERT: B 142 MET cc_start: 0.7194 (mmp) cc_final: 0.6931 (mmp) REVERT: B 175 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: B 287 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6891 (t80) REVERT: B 307 MET cc_start: 0.6590 (mmm) cc_final: 0.5679 (mmm) REVERT: B 480 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8586 (mp) REVERT: B 649 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8192 (t0) REVERT: B 702 MET cc_start: 0.8491 (tpp) cc_final: 0.8254 (tpp) REVERT: B 738 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7675 (t80) REVERT: C 132 SER cc_start: 0.6669 (OUTLIER) cc_final: 0.6020 (m) REVERT: C 198 ASP cc_start: 0.7539 (t0) cc_final: 0.7071 (m-30) REVERT: C 209 MET cc_start: 0.7540 (mpp) cc_final: 0.7054 (tpt) REVERT: C 354 MET cc_start: 0.7797 (mmm) cc_final: 0.7222 (mmm) REVERT: C 392 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: C 470 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6672 (mtm) REVERT: C 494 ASN cc_start: 0.6687 (OUTLIER) cc_final: 0.6084 (p0) REVERT: C 520 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8082 (p0) REVERT: C 780 HIS cc_start: 0.8229 (OUTLIER) cc_final: 0.6313 (m-70) REVERT: C 816 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.7991 (m) REVERT: D 393 THR cc_start: 0.6008 (OUTLIER) cc_final: 0.5708 (p) REVERT: D 637 TRP cc_start: 0.7850 (OUTLIER) cc_final: 0.7064 (m-90) outliers start: 120 outliers final: 75 residues processed: 280 average time/residue: 0.3039 time to fit residues: 143.2148 Evaluate side-chains 271 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 176 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 694 ASN Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 360 LYS Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 TRP Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 637 TRP Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 717 SER Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 16 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 305 optimal weight: 0.7980 chunk 109 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 256 optimal weight: 40.0000 chunk 246 optimal weight: 20.0000 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 ASN D 721 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.113283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.086285 restraints weight = 81811.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.082982 restraints weight = 58030.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.083959 restraints weight = 57195.711| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24840 Z= 0.225 Angle : 0.625 10.830 33763 Z= 0.315 Chirality : 0.045 0.232 3841 Planarity : 0.004 0.038 4289 Dihedral : 4.422 54.772 3463 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.38 % Favored : 91.46 % Rotamer: Outliers : 4.67 % Allowed : 29.84 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % 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: -1.34 (0.15), residues: 3102 helix: 0.28 (0.16), residues: 1192 sheet: -1.13 (0.29), residues: 334 loop : -1.78 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 637 HIS 0.012 0.001 HIS A 780 PHE 0.038 0.002 PHE D 117 TYR 0.031 0.002 TYR A 456 ARG 0.020 0.000 ARG C 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00936 ( 3) link_NAG-ASN : angle 3.75147 ( 9) hydrogen bonds : bond 0.03870 ( 836) hydrogen bonds : angle 5.13454 ( 2418) SS BOND : bond 0.00368 ( 15) SS BOND : angle 1.20073 ( 30) covalent geometry : bond 0.00526 (24822) covalent geometry : angle 0.62165 (33724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 181 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8080 (pp30) REVERT: A 233 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7711 (ttm110) REVERT: A 237 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7731 (tmm) REVERT: A 238 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9029 (tp) REVERT: A 470 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8270 (ttm) REVERT: A 555 MET cc_start: 0.8204 (mtp) cc_final: 0.8001 (mtp) REVERT: A 780 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.7654 (m170) REVERT: B 142 MET cc_start: 0.7288 (mmp) cc_final: 0.6995 (mmp) REVERT: B 175 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6443 (m-80) REVERT: B 184 ASN cc_start: 0.8782 (m-40) cc_final: 0.8542 (m-40) REVERT: B 287 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6951 (t80) REVERT: B 307 MET cc_start: 0.6702 (mmm) cc_final: 0.5820 (mmm) REVERT: B 480 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 702 MET cc_start: 0.8486 (tpp) cc_final: 0.8271 (tpp) REVERT: B 738 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7763 (t80) REVERT: C 132 SER cc_start: 0.6776 (OUTLIER) cc_final: 0.6083 (m) REVERT: C 209 MET cc_start: 0.7526 (mpp) cc_final: 0.7011 (tpt) REVERT: C 354 MET cc_start: 0.7913 (mmm) cc_final: 0.7418 (mmm) REVERT: C 494 ASN cc_start: 0.6649 (OUTLIER) cc_final: 0.6074 (p0) REVERT: C 502 MET cc_start: 0.7832 (mmm) cc_final: 0.7052 (mmt) REVERT: C 520 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8129 (p0) REVERT: C 780 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.6480 (m-70) REVERT: C 816 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.8036 (m) REVERT: D 393 THR cc_start: 0.5865 (OUTLIER) cc_final: 0.5568 (p) REVERT: D 637 TRP cc_start: 0.7899 (OUTLIER) cc_final: 0.7068 (m-90) outliers start: 120 outliers final: 74 residues processed: 285 average time/residue: 0.3074 time to fit residues: 148.9828 Evaluate side-chains 268 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 177 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 694 ASN Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 321 PHE Chi-restraints excluded: chain C residue 360 LYS Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 TRP Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 637 TRP Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 717 SER Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 237 optimal weight: 20.0000 chunk 149 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 246 optimal weight: 30.0000 chunk 184 optimal weight: 8.9990 chunk 284 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 277 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.113725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.088798 restraints weight = 82230.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.089927 restraints weight = 91026.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.089586 restraints weight = 45411.848| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24840 Z= 0.188 Angle : 0.609 11.344 33763 Z= 0.306 Chirality : 0.045 0.235 3841 Planarity : 0.003 0.038 4289 Dihedral : 4.414 53.694 3463 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.83 % Favored : 92.01 % Rotamer: Outliers : 4.32 % Allowed : 30.70 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % 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: -1.34 (0.15), residues: 3102 helix: 0.31 (0.16), residues: 1188 sheet: -1.16 (0.29), residues: 334 loop : -1.81 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 272 HIS 0.009 0.001 HIS A 780 PHE 0.034 0.002 PHE A 583 TYR 0.027 0.001 TYR A 456 ARG 0.013 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.01057 ( 3) link_NAG-ASN : angle 3.77067 ( 9) hydrogen bonds : bond 0.03651 ( 836) hydrogen bonds : angle 5.04320 ( 2418) SS BOND : bond 0.00358 ( 15) SS BOND : angle 1.23195 ( 30) covalent geometry : bond 0.00439 (24822) covalent geometry : angle 0.60535 (33724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 181 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7471 (ttm110) REVERT: A 470 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8163 (ttm) REVERT: A 491 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7554 (p0) REVERT: A 502 MET cc_start: 0.8159 (mmm) cc_final: 0.7813 (mmp) REVERT: A 780 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7660 (m170) REVERT: B 142 MET cc_start: 0.7156 (mmp) cc_final: 0.6953 (mmp) REVERT: B 175 TYR cc_start: 0.6726 (OUTLIER) cc_final: 0.6201 (m-80) REVERT: B 184 ASN cc_start: 0.8651 (m-40) cc_final: 0.8434 (m-40) REVERT: B 287 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6858 (t80) REVERT: B 480 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8664 (mp) REVERT: B 702 MET cc_start: 0.8052 (tpp) cc_final: 0.7847 (tpp) REVERT: B 738 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7764 (t80) REVERT: C 132 SER cc_start: 0.6397 (OUTLIER) cc_final: 0.5605 (m) REVERT: C 198 ASP cc_start: 0.7424 (t0) cc_final: 0.7074 (m-30) REVERT: C 209 MET cc_start: 0.7195 (mpp) cc_final: 0.6928 (tpt) REVERT: C 237 MET cc_start: 0.5334 (pmm) cc_final: 0.5018 (ptp) REVERT: C 494 ASN cc_start: 0.6694 (OUTLIER) cc_final: 0.6176 (p0) REVERT: C 502 MET cc_start: 0.7908 (mmm) cc_final: 0.7093 (mmt) REVERT: C 520 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8063 (p0) REVERT: C 780 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.6613 (m-70) REVERT: C 816 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8038 (m) REVERT: D 112 VAL cc_start: 0.2005 (OUTLIER) cc_final: 0.1556 (t) REVERT: D 187 PHE cc_start: 0.6757 (p90) cc_final: 0.6484 (p90) REVERT: D 393 THR cc_start: 0.6034 (OUTLIER) cc_final: 0.5826 (p) REVERT: D 637 TRP cc_start: 0.7938 (OUTLIER) cc_final: 0.6963 (m-90) outliers start: 111 outliers final: 74 residues processed: 277 average time/residue: 0.3014 time to fit residues: 140.7687 Evaluate side-chains 268 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 178 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 694 ASN Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 360 LYS Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 TRP Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 637 TRP Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 717 SER Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 160 optimal weight: 6.9990 chunk 188 optimal weight: 0.0470 chunk 261 optimal weight: 0.0570 chunk 243 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 126 optimal weight: 0.2980 chunk 111 optimal weight: 0.5980 chunk 267 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.115292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.087778 restraints weight = 82087.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.085140 restraints weight = 57995.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.086285 restraints weight = 48750.956| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24840 Z= 0.106 Angle : 0.585 11.629 33763 Z= 0.292 Chirality : 0.043 0.235 3841 Planarity : 0.003 0.039 4289 Dihedral : 4.188 47.590 3463 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.71 % Favored : 93.13 % Rotamer: Outliers : 2.84 % Allowed : 31.98 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % 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: -1.21 (0.15), residues: 3102 helix: 0.46 (0.16), residues: 1195 sheet: -1.06 (0.30), residues: 319 loop : -1.77 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 272 HIS 0.006 0.001 HIS A 53 PHE 0.037 0.001 PHE A 583 TYR 0.023 0.001 TYR B 579 ARG 0.008 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.01235 ( 3) link_NAG-ASN : angle 3.98037 ( 9) hydrogen bonds : bond 0.03157 ( 836) hydrogen bonds : angle 4.83916 ( 2418) SS BOND : bond 0.00190 ( 15) SS BOND : angle 1.08667 ( 30) covalent geometry : bond 0.00231 (24822) covalent geometry : angle 0.58106 (33724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 191 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7661 (ttm110) REVERT: A 491 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7129 (p0) REVERT: B 175 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: B 287 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6922 (t80) REVERT: B 480 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8603 (mp) REVERT: B 702 MET cc_start: 0.8442 (tpp) cc_final: 0.8234 (tpp) REVERT: B 793 GLU cc_start: 0.7586 (tp30) cc_final: 0.7377 (tp30) REVERT: C 198 ASP cc_start: 0.7520 (t0) cc_final: 0.7150 (m-30) REVERT: C 209 MET cc_start: 0.7561 (mpp) cc_final: 0.7100 (tpt) REVERT: C 494 ASN cc_start: 0.6593 (OUTLIER) cc_final: 0.6013 (p0) REVERT: C 502 MET cc_start: 0.7623 (mmm) cc_final: 0.7416 (mmt) REVERT: C 520 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.7976 (p0) REVERT: C 780 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.6155 (m-70) REVERT: C 816 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7977 (m) REVERT: D 112 VAL cc_start: 0.2088 (OUTLIER) cc_final: 0.1599 (t) REVERT: D 393 THR cc_start: 0.5949 (OUTLIER) cc_final: 0.5645 (p) REVERT: D 637 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.6797 (m-90) outliers start: 73 outliers final: 49 residues processed: 253 average time/residue: 0.3091 time to fit residues: 132.2245 Evaluate side-chains 241 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 180 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 694 ASN Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 360 LYS Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 TRP Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 637 TRP Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 211 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 224 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 273 ASN ** 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 = 0.4203 r_free = 0.4203 target = 0.114681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.087738 restraints weight = 81375.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.086226 restraints weight = 62736.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.087573 restraints weight = 52742.561| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 : 0.003 0.037 24840 Z= 0.123 Angle : 0.590 10.987 33763 Z= 0.293 Chirality : 0.043 0.237 3841 Planarity : 0.003 0.038 4289 Dihedral : 4.140 48.538 3463 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.19 % Favored : 92.65 % Rotamer: Outliers : 2.80 % Allowed : 32.06 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % 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: -1.17 (0.15), residues: 3102 helix: 0.50 (0.16), residues: 1195 sheet: -1.06 (0.30), residues: 319 loop : -1.76 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 272 HIS 0.006 0.001 HIS A 780 PHE 0.037 0.001 PHE A 583 TYR 0.018 0.001 TYR B 579 ARG 0.008 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.01004 ( 3) link_NAG-ASN : angle 3.85991 ( 9) hydrogen bonds : bond 0.03210 ( 836) hydrogen bonds : angle 4.80819 ( 2418) SS BOND : bond 0.00212 ( 15) SS BOND : angle 1.03320 ( 30) covalent geometry : bond 0.00284 (24822) covalent geometry : angle 0.58666 (33724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7375.64 seconds wall clock time: 130 minutes 32.62 seconds (7832.62 seconds total)