Starting phenix.real_space_refine on Wed Jun 25 14:38:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y87_39036/06_2025/8y87_39036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y87_39036/06_2025/8y87_39036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y87_39036/06_2025/8y87_39036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y87_39036/06_2025/8y87_39036.map" model { file = "/net/cci-nas-00/data/ceres_data/8y87_39036/06_2025/8y87_39036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y87_39036/06_2025/8y87_39036.cif" } resolution = 3.26 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 179 5.16 5 C 18832 2.51 5 N 4799 2.21 5 O 5721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 1.31s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29531 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9117 Classifications: {'peptide': 1172} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1115} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "T" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1727 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 14, 'TRANS': 222} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 9121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9121 Classifications: {'peptide': 1184} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 52, 'TRANS': 1128} Chain breaks: 4 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 9163 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1185, 9152 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1128} Chain breaks: 3 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Conformer: "B" Number of residues, atoms: 1185, 9152 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1128} Chain breaks: 3 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 bond proxies already assigned to first conformer: 9365 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" 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: "F" 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE B 633 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 633 " occ=0.50 Time building chain proxies: 22.71, per 1000 atoms: 0.77 Number of scatterers: 29531 At special positions: 0 Unit cell: (158.26, 142.68, 235.34, 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 179 16.00 O 5721 8.00 N 4799 7.00 C 18832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS T 410 " - pdb=" SG CYS T 426 " distance=2.03 Simple disulfide: pdb=" SG CYS T 437 " - pdb=" SG CYS T 465 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 188 " " NAG A1302 " - " ASN A 192 " " NAG A1303 " - " ASN A 335 " " NAG A1304 " - " ASN A 664 " " NAG A1305 " - " ASN A 703 " " NAG A1306 " - " ASN A 725 " " NAG A1307 " - " ASN A 793 " " NAG A1308 " - " ASN A 355 " " NAG A1309 " - " ASN A1211 " " NAG B1301 " - " ASN B 664 " " NAG B1302 " - " ASN B 58 " " NAG B1303 " - " ASN B 188 " " NAG B1304 " - " ASN B 192 " " NAG B1305 " - " ASN B 725 " " NAG B1306 " - " ASN B1211 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 664 " " NAG C1303 " - " ASN C 703 " " NAG C1304 " - " ASN C 771 " " NAG C1305 " - " ASN C 793 " " NAG C1306 " - " ASN C 192 " " NAG C1307 " - " ASN C 355 " " NAG D 1 " - " ASN C 132 " " NAG E 1 " - " ASN C 188 " " NAG F 1 " - " ASN B 132 " Time building additional restraints: 7.47 Conformation dependent library (CDL) restraints added in 5.1 seconds 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 66 sheets defined 23.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.557A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 4.113A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.885A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.584A pdb=" N SER A 412 " --> pdb=" O PHE A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.661A pdb=" N VAL A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 482 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 482' Processing helix chain 'A' and resid 696 through 704 removed outlier: 4.756A pdb=" N ASN A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.546A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 862 removed outlier: 3.615A pdb=" N CYS A 836 " --> pdb=" O TYR A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 878 through 882 removed outlier: 4.165A pdb=" N ASN A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 901 through 909 removed outlier: 3.799A pdb=" N LEU A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.885A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.997A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.794A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1019 removed outlier: 3.565A pdb=" N ASN A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1045 Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.551A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1058 through 1063 Processing helix chain 'A' and resid 1066 through 1069 Processing helix chain 'A' and resid 1070 through 1114 removed outlier: 3.696A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'T' and resid 299 through 303 Processing helix chain 'T' and resid 304 through 307 Processing helix chain 'T' and resid 406 through 411 Processing helix chain 'T' and resid 480 through 492 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 335 removed outlier: 3.572A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 removed outlier: 4.000A pdb=" N TRP C 344 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.546A pdb=" N VAL C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 398 through 402 removed outlier: 3.902A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.866A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.541A pdb=" N PHE C 572 " --> pdb=" O PRO C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 701 removed outlier: 3.530A pdb=" N LEU C 701 " --> pdb=" O CYS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 818 removed outlier: 3.619A pdb=" N VAL C 818 " --> pdb=" O CYS C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 830 removed outlier: 3.508A pdb=" N HIS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 862 removed outlier: 3.537A pdb=" N ASN C 840 " --> pdb=" O CYS C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 909 Processing helix chain 'C' and resid 914 through 924 removed outlier: 3.966A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 940 Processing helix chain 'C' and resid 953 through 965 Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.748A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 3.512A pdb=" N ALA C1005 " --> pdb=" O GLN C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1021 No H-bonds generated for 'chain 'C' and resid 1019 through 1021' Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.882A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.528A pdb=" N ASN C1049 " --> pdb=" O GLN C1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1057 through 1063 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 5.083A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.893A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.787A pdb=" N ILE B 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 375 through 379' Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.576A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 442 through 448 removed outlier: 4.004A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.509A pdb=" N ASN B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.590A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 701 Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 835 through 862 removed outlier: 4.077A pdb=" N ILE B 839 " --> pdb=" O PHE B 835 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 844 " --> pdb=" O ASN B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 910 removed outlier: 3.679A pdb=" N LEU B 906 " --> pdb=" O PRO B 902 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 923 removed outlier: 3.562A pdb=" N PHE B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 923 " --> pdb=" O VAL B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 928 removed outlier: 4.593A pdb=" N GLY B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 4.176A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 964 removed outlier: 3.797A pdb=" N ALA B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 964 " --> pdb=" O THR B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.893A pdb=" N PHE B 968 " --> pdb=" O ALA B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 978 through 989 removed outlier: 3.622A pdb=" N GLY B 989 " --> pdb=" O TYR B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 998 removed outlier: 3.512A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1018 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.847A pdb=" N LYS B1028 " --> pdb=" O SER B1024 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1057 through 1063 removed outlier: 3.541A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1069 Processing helix chain 'B' and resid 1070 through 1114 removed outlier: 4.248A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 67 removed outlier: 3.527A pdb=" N PHE A 67 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 262 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.527A pdb=" N ARG A 75 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 211 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.709A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 112 Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.756A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.518A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 319 removed outlier: 6.729A pdb=" N VAL A 317 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.301A pdb=" N THR A 435 " --> pdb=" O VAL A 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.983A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.983A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.710A pdb=" N PHE A 354 " --> pdb=" O CYS A 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 460 through 463 Processing sheet with id=AB5, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.684A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 538 " --> pdb=" O CYS A 466 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.774A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 724 through 725 removed outlier: 6.482A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.056A pdb=" N SER A 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 786 through 791 Processing sheet with id=AC1, first strand: chain 'A' and resid 794 through 803 removed outlier: 3.744A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.127A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 866 through 868 removed outlier: 6.882A pdb=" N LEU A 867 " --> pdb=" O VAL B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 3.699A pdb=" N CYS A1163 " --> pdb=" O THR A1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 1170 through 1172 Processing sheet with id=AC6, first strand: chain 'A' and resid 1175 through 1179 Processing sheet with id=AC7, first strand: chain 'T' and resid 260 through 261 removed outlier: 4.525A pdb=" N ASN T 398 " --> pdb=" O GLY T 383 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY T 383 " --> pdb=" O ASN T 398 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU T 378 " --> pdb=" O SER T 448 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER T 448 " --> pdb=" O LEU T 378 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL T 446 " --> pdb=" O TRP T 380 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS T 449 " --> pdb=" O ILE T 452 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 260 through 261 removed outlier: 4.617A pdb=" N CYS T 426 " --> pdb=" O ILE T 405 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL T 473 " --> pdb=" O SER T 460 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER T 460 " --> pdb=" O VAL T 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 278 through 283 removed outlier: 5.301A pdb=" N HIS T 279 " --> pdb=" O VAL T 275 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL T 275 " --> pdb=" O HIS T 279 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS T 281 " --> pdb=" O LEU T 273 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS T 350 " --> pdb=" O GLU T 329 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL T 331 " --> pdb=" O LEU T 348 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU T 348 " --> pdb=" O VAL T 331 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 35 through 36 removed outlier: 4.258A pdb=" N ILE C 35 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 75 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP C 257 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 105 " --> pdb=" O TRP C 257 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY C 101 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 61 through 68 removed outlier: 3.955A pdb=" N ASN C 278 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.658A pdb=" N GLY C 81 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.710A pdb=" N SER C 96 " --> pdb=" O TYR C 235 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 235 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 125 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.896A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 120 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AD8, first strand: chain 'C' and resid 316 through 319 removed outlier: 4.121A pdb=" N ARG C 319 " --> pdb=" O ASP C 623 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 629 " --> pdb=" O TYR C 622 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 55 " --> pdb=" O LEU C 647 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 345 through 349 removed outlier: 4.510A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 390 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 386 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN C 595 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 368 through 371 Processing sheet with id=AE2, first strand: chain 'C' and resid 460 through 463 Processing sheet with id=AE3, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.676A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 773 through 775 removed outlier: 5.852A pdb=" N SER C 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 786 through 791 Processing sheet with id=AE6, first strand: chain 'C' and resid 794 through 804 removed outlier: 3.644A pdb=" N LEU C1131 " --> pdb=" O PHE C1146 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 809 through 811 removed outlier: 4.238A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 878 through 879 removed outlier: 3.642A pdb=" N VAL C 879 " --> pdb=" O ILE C 882 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.501A pdb=" N ILE C1170 " --> pdb=" O LEU C1162 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1175 through 1179 Processing sheet with id=AF2, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.814A pdb=" N ASN B 26 " --> pdb=" O LEU B 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'B' and resid 35 through 39 removed outlier: 5.375A pdb=" N ASP B 38 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 62 through 68 removed outlier: 4.033A pdb=" N GLY B 101 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 199 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 214 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 62 through 68 removed outlier: 4.031A pdb=" N ASN B 278 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 110 through 113 Processing sheet with id=AF7, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.682A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 187 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 148 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 161 through 162 removed outlier: 6.452A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AG1, first strand: chain 'B' and resid 317 through 319 removed outlier: 3.665A pdb=" N LYS B 665 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AG3, first strand: chain 'B' and resid 346 through 349 removed outlier: 6.706A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 459 through 462 Processing sheet with id=AG5, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.627A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 504 through 506 Processing sheet with id=AG7, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AG8, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.047A pdb=" N ASN B 725 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE B 764 " --> pdb=" O ASN B 725 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 766 " --> pdb=" O THR B 727 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR B 729 " --> pdb=" O THR B 766 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.776A pdb=" N SER B1152 " --> pdb=" O THR B 792 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE B 794 " --> pdb=" O PRO B1150 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE B 796 " --> pdb=" O TYR B1148 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR B1148 " --> pdb=" O ILE B 796 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY B 798 " --> pdb=" O PHE B1146 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE B1146 " --> pdb=" O GLY B 798 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU B 800 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B1144 " --> pdb=" O GLU B 800 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 802 " --> pdb=" O LEU B1142 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B1142 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN B 804 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY B1140 " --> pdb=" O GLN B 804 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B1131 " --> pdb=" O PHE B1146 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR B1148 " --> pdb=" O HIS B1129 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS B1129 " --> pdb=" O TYR B1148 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.093A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.657A pdb=" N ILE B1170 " --> pdb=" O LEU B1162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B1162 " --> pdb=" O ILE B1170 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 1175 through 1179 975 hydrogen bonds defined for protein. 2683 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: 14.67 Time building geometry restraints manager: 8.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9392 1.34 - 1.46: 7458 1.46 - 1.58: 13188 1.58 - 1.70: 0 1.70 - 1.81: 211 Bond restraints: 30249 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 30244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 40757 1.71 - 3.41: 465 3.41 - 5.12: 21 5.12 - 6.83: 8 6.83 - 8.54: 2 Bond angle restraints: 41253 Sorted by residual: angle pdb=" CA LEU C 521 " pdb=" CB LEU C 521 " pdb=" CG LEU C 521 " ideal model delta sigma weight residual 116.30 124.84 -8.54 3.50e+00 8.16e-02 5.95e+00 angle pdb=" C SER C 519 " pdb=" N CYS C 520 " pdb=" CA CYS C 520 " ideal model delta sigma weight residual 122.07 125.31 -3.24 1.43e+00 4.89e-01 5.15e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.77 6.18 3.00e+00 1.11e-01 4.24e+00 angle pdb=" C ASN C 53 " pdb=" N ARG C 54 " pdb=" CA ARG C 54 " ideal model delta sigma weight residual 121.87 126.26 -4.39 2.24e+00 1.99e-01 3.84e+00 angle pdb=" CA PRO A1067 " pdb=" C PRO A1067 " pdb=" N PRO A1068 " ideal model delta sigma weight residual 117.93 120.28 -2.35 1.20e+00 6.94e-01 3.82e+00 ... (remaining 41248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 17979 21.79 - 43.58: 322 43.58 - 65.38: 32 65.38 - 87.17: 6 87.17 - 108.96: 4 Dihedral angle restraints: 18343 sinusoidal: 7287 harmonic: 11056 Sorted by residual: dihedral pdb=" CB CYS A 925 " pdb=" SG CYS A 925 " pdb=" SG CYS A 936 " pdb=" CB CYS A 936 " ideal model delta sinusoidal sigma weight residual 93.00 138.96 -45.96 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.75 108.96 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C3 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.26 106.88 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 18340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3987 0.054 - 0.108: 665 0.108 - 0.161: 102 0.161 - 0.215: 0 0.215 - 0.269: 1 Chirality restraints: 4755 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CG LEU C 521 " pdb=" CB LEU C 521 " pdb=" CD1 LEU C 521 " pdb=" CD2 LEU C 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1211 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 4752 not shown) Planarity restraints: 5311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 91 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO B 92 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 92 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 92 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1066 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A1067 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1067 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1067 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO B1067 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " -0.019 5.00e-02 4.00e+02 ... (remaining 5308 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 5345 2.78 - 3.31: 26799 3.31 - 3.84: 46158 3.84 - 4.37: 52054 4.37 - 4.90: 93700 Nonbonded interactions: 224056 Sorted by model distance: nonbonded pdb=" OD1 ASN C 355 " pdb=" OG1 THR C 358 " model vdw 2.244 3.040 nonbonded pdb=" O GLN B1180 " pdb=" OG SER B1183 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR C 832 " pdb=" OD1 ASP C1075 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR A 448 " pdb=" O PHE A 473 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR A 123 " pdb=" O VAL A 139 " model vdw 2.274 3.040 ... (remaining 224051 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 14 through 19 or resid 21 through 24 or (resid 25 and (nam \ e N or name CA or name C or name O or name CB )) or resid 26 or (resid 34 and (n \ ame N or name CA or name C or name O or name CB )) or resid 35 through 79 or (re \ sid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thro \ ugh 83 or (resid 84 and (name N or name CA or name C or name O or name CB )) or \ resid 85 through 90 or (resid 91 and (name N or name CA or name C or name O or n \ ame CB )) or resid 92 through 109 or (resid 110 and (name N or name CA or name C \ or name O or name CB )) or resid 111 or (resid 112 and (name N or name CA or na \ me C or name O or name CB )) or resid 113 or (resid 114 through 115 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 117 or (resid \ 118 and (name N or name CA or name C or name O or name CB )) or resid 119 throug \ h 139 or (resid 140 and (name N or name CA or name C or name O or name CB )) or \ resid 141 through 156 or (resid 157 and (name N or name CA or name C or name O o \ r name CB )) or resid 158 through 163 or (resid 164 and (name N or name CA or na \ me C or name O or name CB )) or resid 165 or (resid 166 and (name N or name CA o \ r name C or name O or name CB )) or resid 167 through 173 or (resid 174 and (nam \ e N or name CA or name C or name O or name CB )) or resid 175 through 179 or (re \ sid 180 and (name N or name CA or name C or name O or name CB )) or resid 181 th \ rough 185 or (resid 186 and (name N or name CA or name C or name O or name CB )) \ or resid 187 through 205 or (resid 206 and (name N or name CA or name C or name \ O or name CB )) or resid 207 through 244 or resid 254 through 416 or (resid 417 \ and (name N or name CA or name C or name O or name CB )) or resid 418 through 4 \ 91 or (resid 492 through 493 and (name N or name CA or name C or name O or name \ CB )) or resid 494 through 522 or (resid 523 and (name N or name CA or name C or \ name O or name CB )) or resid 524 through 551 or (resid 552 and (name N or name \ CA or name C or name O or name CB )) or resid 553 or (resid 554 and (name N or \ name CA or name C or name O or name CB )) or resid 555 through 557 or resid 563 \ through 572 or (resid 573 and (name N or name CA or name C or name O or name CB \ )) or resid 574 through 615 or (resid 616 and (name N or name CA or name C or na \ me O or name CB )) or resid 617 through 619 or (resid 620 and (name N or name CA \ or name C or name O or name CB )) or resid 621 through 629 or (resid 630 and (n \ ame N or name CA or name C or name O or name CB )) or resid 631 or (resid 632 an \ d (name N or name CA or name C or name O or name CB )) or (resid 634 and (name N \ or name CA or name C or name O or name CB )) or resid 635 through 651 or (resid \ 652 and (name N or name CA or name C or name O or name CB )) or resid 653 or (r \ esid 654 and (name N or name CA or name C or name O or name CB )) or resid 655 t \ hrough 708 or (resid 709 and (name N or name CA or name C or name O or name CB ) \ ) or resid 710 through 779 or (resid 780 and (name N or name CA or name C or nam \ e O or name CB )) or resid 781 through 875 or (resid 876 and (name N or name CA \ or name C or name O or name CB )) or resid 877 through 929 or (resid 930 through \ 932 and (name N or name CA or name C or name O or name CB )) or resid 933 throu \ gh 998 or (resid 999 and (name N or name CA or name C or name O or name CB )) or \ resid 1000 through 1148 or (resid 1149 and (name N or name CA or name C or name \ O or name CB )) or resid 1150 through 1199 or (resid 1200 and (name N or name C \ A or name C or name O or name CB )) or resid 1201 through 1221 or resid 1301 thr \ ough 1306)) selection = (chain 'B' and (resid 14 through 19 or resid 21 through 26 or resid 34 through 1 \ 09 or (resid 110 and (name N or name CA or name C or name O or name CB )) or res \ id 111 through 117 or (resid 118 and (name N or name CA or name C or name O or n \ ame CB )) or resid 119 through 139 or (resid 140 and (name N or name CA or name \ C or name O or name CB )) or resid 141 through 156 or (resid 157 and (name N or \ name CA or name C or name O or name CB )) or resid 158 through 173 or (resid 174 \ and (name N or name CA or name C or name O or name CB )) or resid 175 through 1 \ 85 or (resid 186 and (name N or name CA or name C or name O or name CB )) or res \ id 187 through 235 or resid 237 through 416 or (resid 417 and (name N or name CA \ or name C or name O or name CB )) or resid 418 through 483 or resid 490 through \ 501 or (resid 502 and (name N or name CA or name C or name O or name CB )) or r \ esid 519 through 520 or (resid 521 and (name N or name CA or name C or name O or \ name CB )) or resid 522 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 551 or (resid 552 and (name N or name CA or \ name C or name O or name CB )) or resid 553 through 572 or (resid 573 and (name \ N or name CA or name C or name O or name CB )) or resid 574 through 632 or resi \ d 634 through 705 or (resid 706 and (name N or name CA or name C or name O or na \ me CB )) or resid 707 through 708 or (resid 709 and (name N or name CA or name C \ or name O or name CB )) or resid 710 through 779 or (resid 780 and (name N or n \ ame CA or name C or name O or name CB )) or resid 781 through 929 or (resid 930 \ through 932 and (name N or name CA or name C or name O or name CB )) or resid 93 \ 3 through 998 or (resid 999 and (name N or name CA or name C or name O or name C \ B )) or resid 1000 through 1199 or (resid 1200 and (name N or name CA or name C \ or name O or name CB )) or resid 1201 through 1221 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 79 or (resid 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 through 111 or (resid 112 and \ (name N or name CA or name C or name O or name CB )) or resid 113 or (resid 114 \ through 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 163 or (resid 164 and (name N or name CA or name C or name O or name \ CB )) or resid 165 through 179 or (resid 180 and (name N or name CA or name C or \ name O or name CB )) or resid 181 through 205 or (resid 206 and (name N or name \ CA or name C or name O or name CB )) or resid 207 through 235 or resid 237 thro \ ugh 244 or resid 254 through 311 or (resid 312 and (name N or name CA or name C \ or name O or name CB )) or resid 313 through 483 or resid 490 through 491 or (re \ sid 492 through 493 and (name N or name CA or name C or name O or name CB )) or \ resid 494 through 501 or (resid 502 and (name N or name CA or name C or name O o \ r name CB )) or resid 519 through 520 or (resid 521 and (name N or name CA or na \ me C or name O or name CB )) or resid 522 through 553 or (resid 554 and (name N \ or name CA or name C or name O or name CB )) or resid 555 through 557 or resid 5 \ 63 through 569 or (resid 570 through 571 and (name N or name CA or name C or nam \ e O or name CB )) or resid 572 through 615 or (resid 616 and (name N or name CA \ or name C or name O or name CB )) or resid 617 through 619 or (resid 620 and (na \ me N or name CA or name C or name O or name CB )) or resid 621 through 629 or (r \ esid 630 and (name N or name CA or name C or name O or name CB )) or resid 631 o \ r (resid 632 and (name N or name CA or name C or name O or name CB )) or (resid \ 634 and (name N or name CA or name C or name O or name CB )) or resid 635 throug \ h 651 or (resid 652 and (name N or name CA or name C or name O or name CB )) or \ resid 653 or (resid 654 and (name N or name CA or name C or name O or name CB )) \ or resid 655 through 705 or (resid 706 and (name N or name CA or name C or name \ O or name CB )) or resid 707 through 875 or (resid 876 and (name N or name CA o \ r name C or name O or name CB )) or resid 877 through 930 or (resid 931 through \ 932 and (name N or name CA or name C or name O or name CB )) or resid 933 throug \ h 1148 or (resid 1149 and (name N or name CA or name C or name O or name CB )) o \ r resid 1150 through 1221 or resid 1301 through 1306)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 39.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 78.120 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 : 0.002 0.035 30347 Z= 0.106 Angle : 0.432 8.537 41478 Z= 0.222 Chirality : 0.041 0.269 4755 Planarity : 0.003 0.051 5286 Dihedral : 7.819 108.960 11032 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.77 % Allowed : 4.58 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.12), residues: 3749 helix: 0.01 (0.19), residues: 706 sheet: -0.72 (0.17), residues: 732 loop : -2.50 (0.11), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.000 TRP B 344 HIS 0.003 0.000 HIS B 175 PHE 0.008 0.001 PHE B 209 TYR 0.010 0.001 TYR A1148 ARG 0.002 0.000 ARG B 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 25) link_NAG-ASN : angle 0.90029 ( 75) link_BETA1-4 : bond 0.00475 ( 4) link_BETA1-4 : angle 1.06993 ( 12) hydrogen bonds : bond 0.14182 ( 955) hydrogen bonds : angle 5.15620 ( 2683) SS BOND : bond 0.00097 ( 69) SS BOND : angle 0.46098 ( 138) covalent geometry : bond 0.00208 (30249) covalent geometry : angle 0.43012 (41253) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 803 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8522 (mt) cc_final: 0.8293 (mt) REVERT: A 106 VAL cc_start: 0.8311 (t) cc_final: 0.8040 (m) REVERT: A 186 LYS cc_start: 0.8198 (tttt) cc_final: 0.7832 (tttt) REVERT: A 238 MET cc_start: 0.6263 (ptp) cc_final: 0.5932 (ptp) REVERT: A 293 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8380 (ttmm) REVERT: A 323 ASN cc_start: 0.6538 (p0) cc_final: 0.6256 (p0) REVERT: A 357 SER cc_start: 0.8422 (t) cc_final: 0.8143 (p) REVERT: A 431 LEU cc_start: 0.8412 (mt) cc_final: 0.8202 (mt) REVERT: A 473 PHE cc_start: 0.7636 (t80) cc_final: 0.7426 (t80) REVERT: A 500 LYS cc_start: 0.8302 (ptpt) cc_final: 0.7879 (ptpt) REVERT: A 577 PHE cc_start: 0.6297 (m-10) cc_final: 0.5872 (m-10) REVERT: A 603 CYS cc_start: 0.4680 (m) cc_final: 0.4370 (m) REVERT: A 610 SER cc_start: 0.8402 (t) cc_final: 0.7902 (m) REVERT: A 635 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6645 (tm-30) REVERT: A 661 PHE cc_start: 0.8073 (m-80) cc_final: 0.7799 (m-10) REVERT: A 673 TYR cc_start: 0.7649 (t80) cc_final: 0.7445 (t80) REVERT: A 782 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8463 (p) REVERT: A 806 SER cc_start: 0.8594 (m) cc_final: 0.8322 (t) REVERT: A 827 ASP cc_start: 0.7230 (m-30) cc_final: 0.6818 (m-30) REVERT: A 828 LEU cc_start: 0.8463 (mm) cc_final: 0.8157 (mt) REVERT: A 851 ASP cc_start: 0.7044 (m-30) cc_final: 0.6765 (m-30) REVERT: A 1010 LYS cc_start: 0.8207 (tttt) cc_final: 0.7941 (ttmm) REVERT: A 1048 PHE cc_start: 0.8532 (m-10) cc_final: 0.8290 (m-80) REVERT: A 1054 ILE cc_start: 0.8745 (tp) cc_final: 0.8522 (tp) REVERT: A 1095 ASP cc_start: 0.6991 (m-30) cc_final: 0.6573 (m-30) REVERT: A 1116 SER cc_start: 0.8513 (t) cc_final: 0.7977 (p) REVERT: A 1185 MET cc_start: 0.7270 (mtp) cc_final: 0.6119 (mtp) REVERT: C 66 TYR cc_start: 0.8532 (m-80) cc_final: 0.8331 (m-80) REVERT: C 90 TYR cc_start: 0.8150 (m-80) cc_final: 0.7811 (m-10) REVERT: C 107 LYS cc_start: 0.7860 (tttp) cc_final: 0.7604 (tttp) REVERT: C 338 VAL cc_start: 0.4854 (OUTLIER) cc_final: 0.4627 (p) REVERT: C 353 ASN cc_start: 0.7855 (m-40) cc_final: 0.7494 (m-40) REVERT: C 354 PHE cc_start: 0.7861 (p90) cc_final: 0.7595 (p90) REVERT: C 634 LYS cc_start: 0.7552 (ttmm) cc_final: 0.7347 (ttmm) REVERT: C 647 LEU cc_start: 0.8200 (pp) cc_final: 0.7753 (pp) REVERT: C 711 PHE cc_start: 0.7645 (m-80) cc_final: 0.7422 (m-80) REVERT: C 729 TYR cc_start: 0.7312 (t80) cc_final: 0.6980 (t80) REVERT: C 782 VAL cc_start: 0.9126 (t) cc_final: 0.8772 (m) REVERT: C 845 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6139 (mp0) REVERT: C 848 ASP cc_start: 0.7231 (m-30) cc_final: 0.6845 (m-30) REVERT: C 1056 SER cc_start: 0.8121 (p) cc_final: 0.7869 (t) REVERT: C 1095 ASP cc_start: 0.7477 (t0) cc_final: 0.7148 (t0) REVERT: C 1109 LYS cc_start: 0.8363 (ttmt) cc_final: 0.8081 (tttt) REVERT: C 1112 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6183 (mt-10) REVERT: C 1173 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7867 (mtpp) REVERT: B 124 ILE cc_start: 0.7431 (tt) cc_final: 0.7021 (pt) REVERT: B 133 THR cc_start: 0.7497 (p) cc_final: 0.7293 (p) REVERT: B 147 GLU cc_start: 0.6116 (tm-30) cc_final: 0.5678 (tm-30) REVERT: B 148 ILE cc_start: 0.8013 (mp) cc_final: 0.7770 (tt) REVERT: B 266 TYR cc_start: 0.6997 (m-80) cc_final: 0.6751 (m-80) REVERT: B 324 LEU cc_start: 0.7684 (mt) cc_final: 0.7482 (mp) REVERT: B 651 SER cc_start: 0.8252 (m) cc_final: 0.8037 (m) REVERT: B 702 ASN cc_start: 0.7770 (t0) cc_final: 0.7412 (t0) REVERT: B 878 ASP cc_start: 0.7142 (p0) cc_final: 0.6773 (p0) REVERT: B 883 ASP cc_start: 0.7767 (t0) cc_final: 0.7537 (t0) REVERT: B 905 ASP cc_start: 0.7696 (m-30) cc_final: 0.7428 (m-30) REVERT: B 985 TYR cc_start: 0.8104 (m-10) cc_final: 0.7769 (m-10) REVERT: B 999 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7869 (mtpt) REVERT: B 1038 GLN cc_start: 0.7502 (tp40) cc_final: 0.7198 (tp40) REVERT: B 1060 GLU cc_start: 0.7319 (tt0) cc_final: 0.7078 (tt0) REVERT: B 1090 SER cc_start: 0.8408 (t) cc_final: 0.8176 (m) REVERT: B 1095 ASP cc_start: 0.7313 (t0) cc_final: 0.6867 (t0) REVERT: B 1156 VAL cc_start: 0.8628 (p) cc_final: 0.8302 (m) outliers start: 58 outliers final: 14 residues processed: 845 average time/residue: 0.4117 time to fit residues: 552.2719 Evaluate side-chains 624 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 607 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.5980 chunk 284 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 341 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 140 GLN A 248 ASN A 265 GLN A 291 GLN A 323 ASN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS A 531 ASN A 545 HIS A 683 GLN A 709 GLN A 847 ASN A 854 GLN A 941 ASN A1017 ASN A1045 GLN A1046 GLN A1049 ASN A1071 GLN A1181 ASN T 276 GLN C 335 ASN C 353 ASN C 562 HIS C 591 ASN C 789 GLN C 872 ASN C 881 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 ASN C1000 ASN C1001 GLN C1038 GLN C1059 GLN C1135 GLN B 108 ASN B 152 GLN B 265 GLN B 355 ASN B 395 ASN B 410 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 GLN B 870 ASN B 881 ASN B1059 GLN B1117 GLN B1122 ASN B1145 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.167455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126445 restraints weight = 46631.778| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.60 r_work: 0.3390 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30347 Z= 0.188 Angle : 0.586 11.678 41478 Z= 0.296 Chirality : 0.046 0.266 4755 Planarity : 0.004 0.048 5286 Dihedral : 5.524 68.063 4685 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.93 % Allowed : 11.32 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.60 (0.13), residues: 3749 helix: 0.75 (0.20), residues: 760 sheet: -0.44 (0.17), residues: 744 loop : -2.05 (0.12), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 174 HIS 0.010 0.001 HIS C1145 PHE 0.031 0.002 PHE B 658 TYR 0.027 0.002 TYR B 203 ARG 0.006 0.001 ARG C1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00786 ( 25) link_NAG-ASN : angle 2.74113 ( 75) link_BETA1-4 : bond 0.00442 ( 4) link_BETA1-4 : angle 1.72405 ( 12) hydrogen bonds : bond 0.04712 ( 955) hydrogen bonds : angle 4.46110 ( 2683) SS BOND : bond 0.00444 ( 69) SS BOND : angle 1.74299 ( 138) covalent geometry : bond 0.00439 (30249) covalent geometry : angle 0.56647 (41253) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 632 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.8619 (t) cc_final: 0.8266 (m) REVERT: A 234 HIS cc_start: 0.7726 (m90) cc_final: 0.7347 (m90) REVERT: A 238 MET cc_start: 0.6862 (ptp) cc_final: 0.6544 (ptp) REVERT: A 266 TYR cc_start: 0.8365 (m-10) cc_final: 0.8157 (m-10) REVERT: A 323 ASN cc_start: 0.7299 (p0) cc_final: 0.7064 (p0) REVERT: A 357 SER cc_start: 0.8612 (t) cc_final: 0.8342 (p) REVERT: A 467 PHE cc_start: 0.8934 (m-80) cc_final: 0.8727 (m-80) REVERT: A 473 PHE cc_start: 0.8182 (t80) cc_final: 0.7606 (t80) REVERT: A 500 LYS cc_start: 0.8567 (ptpt) cc_final: 0.8143 (ptpt) REVERT: A 577 PHE cc_start: 0.7980 (m-10) cc_final: 0.7747 (m-10) REVERT: A 610 SER cc_start: 0.8812 (t) cc_final: 0.8238 (m) REVERT: A 632 ILE cc_start: 0.8634 (mt) cc_final: 0.8345 (mp) REVERT: A 635 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 649 TYR cc_start: 0.8091 (m-10) cc_final: 0.7802 (m-10) REVERT: A 667 TYR cc_start: 0.8328 (m-80) cc_final: 0.7916 (m-80) REVERT: A 673 TYR cc_start: 0.8202 (t80) cc_final: 0.7925 (t80) REVERT: A 782 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8554 (p) REVERT: A 806 SER cc_start: 0.8878 (m) cc_final: 0.8606 (t) REVERT: A 827 ASP cc_start: 0.8248 (m-30) cc_final: 0.8043 (t0) REVERT: A 828 LEU cc_start: 0.8769 (mm) cc_final: 0.8433 (mp) REVERT: A 863 GLN cc_start: 0.8081 (tp40) cc_final: 0.7814 (tt0) REVERT: A 1003 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7883 (tt) REVERT: A 1010 LYS cc_start: 0.8430 (tttt) cc_final: 0.8112 (ttmm) REVERT: A 1091 GLN cc_start: 0.7929 (mt0) cc_final: 0.7476 (mt0) REVERT: A 1095 ASP cc_start: 0.7759 (m-30) cc_final: 0.7281 (m-30) REVERT: A 1116 SER cc_start: 0.8777 (t) cc_final: 0.8276 (p) REVERT: A 1185 MET cc_start: 0.8455 (mtp) cc_final: 0.8245 (mtp) REVERT: C 74 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7705 (t80) REVERT: C 86 SER cc_start: 0.8574 (t) cc_final: 0.8355 (p) REVERT: C 105 LYS cc_start: 0.8404 (tttt) cc_final: 0.8198 (tttp) REVERT: C 128 SER cc_start: 0.8949 (p) cc_final: 0.8700 (m) REVERT: C 384 ASN cc_start: 0.8519 (m-40) cc_final: 0.8247 (m-40) REVERT: C 634 LYS cc_start: 0.8262 (ttmm) cc_final: 0.8042 (tttm) REVERT: C 649 TYR cc_start: 0.8706 (m-80) cc_final: 0.8424 (m-10) REVERT: C 674 SER cc_start: 0.8390 (t) cc_final: 0.8169 (p) REVERT: C 711 PHE cc_start: 0.8292 (m-80) cc_final: 0.7906 (m-80) REVERT: C 845 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: C 1001 GLN cc_start: 0.8787 (mt0) cc_final: 0.8561 (mt0) REVERT: C 1068 PRO cc_start: 0.7776 (Cg_exo) cc_final: 0.7369 (Cg_endo) REVERT: C 1095 ASP cc_start: 0.8335 (t0) cc_final: 0.7962 (t0) REVERT: C 1183 SER cc_start: 0.8347 (t) cc_final: 0.7649 (p) REVERT: C 1205 MET cc_start: 0.7863 (ptp) cc_final: 0.7647 (ptp) REVERT: C 1214 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8664 (mtpp) REVERT: B 41 ASP cc_start: 0.8138 (t0) cc_final: 0.7708 (t70) REVERT: B 124 ILE cc_start: 0.7636 (tt) cc_final: 0.7064 (pt) REVERT: B 148 ILE cc_start: 0.8173 (mp) cc_final: 0.7830 (tt) REVERT: B 233 SER cc_start: 0.7760 (m) cc_final: 0.6923 (p) REVERT: B 237 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6741 (p) REVERT: B 266 TYR cc_start: 0.7751 (m-80) cc_final: 0.7514 (m-10) REVERT: B 320 ARG cc_start: 0.7876 (ttm170) cc_final: 0.7530 (mtt-85) REVERT: B 467 PHE cc_start: 0.8527 (m-80) cc_final: 0.8317 (m-10) REVERT: B 702 ASN cc_start: 0.8144 (t0) cc_final: 0.7791 (t0) REVERT: B 729 TYR cc_start: 0.8251 (t80) cc_final: 0.7746 (t80) REVERT: B 745 ASP cc_start: 0.7902 (t0) cc_final: 0.7431 (t0) REVERT: B 746 TYR cc_start: 0.8335 (t80) cc_final: 0.8021 (t80) REVERT: B 862 MET cc_start: 0.7714 (tpt) cc_final: 0.7513 (tpt) REVERT: B 878 ASP cc_start: 0.7872 (p0) cc_final: 0.7618 (p0) REVERT: B 883 ASP cc_start: 0.8462 (t0) cc_final: 0.8175 (t0) REVERT: B 912 LYS cc_start: 0.8493 (ptmt) cc_final: 0.8118 (ptmt) REVERT: B 958 TYR cc_start: 0.8420 (m-10) cc_final: 0.8191 (m-80) REVERT: B 999 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8287 (mtpt) REVERT: B 1038 GLN cc_start: 0.8415 (tp40) cc_final: 0.8051 (tp40) REVERT: B 1060 GLU cc_start: 0.8409 (tt0) cc_final: 0.8012 (tt0) REVERT: B 1064 ARG cc_start: 0.8933 (mtp180) cc_final: 0.8697 (mtp-110) REVERT: B 1090 SER cc_start: 0.8780 (t) cc_final: 0.8545 (m) REVERT: B 1095 ASP cc_start: 0.8036 (t0) cc_final: 0.7672 (t0) REVERT: B 1156 VAL cc_start: 0.8709 (p) cc_final: 0.8344 (m) REVERT: B 1212 PHE cc_start: 0.7264 (m-10) cc_final: 0.6459 (m-80) outliers start: 96 outliers final: 53 residues processed: 685 average time/residue: 0.4067 time to fit residues: 449.6997 Evaluate side-chains 632 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 574 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 998 ASN Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 881 ASN Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1200 LYS Chi-restraints excluded: chain B residue 1205 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 327 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 122 optimal weight: 30.0000 chunk 78 optimal weight: 0.9980 chunk 127 optimal weight: 50.0000 chunk 160 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 595 ASN A 909 ASN C 353 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 ASN C1135 GLN C1201 ASN B 152 GLN B 201 HIS ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN B1135 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.165284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123771 restraints weight = 46562.251| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.59 r_work: 0.3339 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30347 Z= 0.185 Angle : 0.567 9.975 41478 Z= 0.288 Chirality : 0.045 0.277 4755 Planarity : 0.004 0.049 5286 Dihedral : 5.065 57.977 4681 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.36 % Allowed : 12.67 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.32 (0.13), residues: 3749 helix: 1.08 (0.20), residues: 764 sheet: -0.31 (0.17), residues: 767 loop : -1.90 (0.12), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 197 HIS 0.009 0.001 HIS C1145 PHE 0.026 0.002 PHE B 658 TYR 0.022 0.002 TYR C 49 ARG 0.006 0.001 ARG A1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 25) link_NAG-ASN : angle 2.39789 ( 75) link_BETA1-4 : bond 0.00447 ( 4) link_BETA1-4 : angle 1.60436 ( 12) hydrogen bonds : bond 0.04907 ( 955) hydrogen bonds : angle 4.50170 ( 2683) SS BOND : bond 0.00314 ( 69) SS BOND : angle 1.67248 ( 138) covalent geometry : bond 0.00431 (30249) covalent geometry : angle 0.54984 (41253) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 593 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 HIS cc_start: 0.7804 (m90) cc_final: 0.7443 (m90) REVERT: A 238 MET cc_start: 0.6866 (ptp) cc_final: 0.6559 (ptp) REVERT: A 323 ASN cc_start: 0.7472 (p0) cc_final: 0.7199 (p0) REVERT: A 357 SER cc_start: 0.8626 (t) cc_final: 0.8397 (p) REVERT: A 366 ASP cc_start: 0.7730 (t0) cc_final: 0.7398 (t0) REVERT: A 473 PHE cc_start: 0.8266 (t80) cc_final: 0.7678 (t80) REVERT: A 500 LYS cc_start: 0.8535 (ptpt) cc_final: 0.8087 (ptpt) REVERT: A 555 LYS cc_start: 0.8339 (tppp) cc_final: 0.7906 (tppp) REVERT: A 577 PHE cc_start: 0.8162 (m-10) cc_final: 0.7952 (m-10) REVERT: A 610 SER cc_start: 0.8904 (t) cc_final: 0.8358 (m) REVERT: A 632 ILE cc_start: 0.8656 (mt) cc_final: 0.8355 (mp) REVERT: A 635 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 649 TYR cc_start: 0.8113 (m-10) cc_final: 0.7822 (m-10) REVERT: A 667 TYR cc_start: 0.8429 (m-80) cc_final: 0.8041 (m-80) REVERT: A 768 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8281 (mm-30) REVERT: A 806 SER cc_start: 0.8876 (m) cc_final: 0.8664 (t) REVERT: A 827 ASP cc_start: 0.8293 (m-30) cc_final: 0.8005 (m-30) REVERT: A 828 LEU cc_start: 0.8777 (mm) cc_final: 0.8450 (mp) REVERT: A 863 GLN cc_start: 0.8274 (tp40) cc_final: 0.8042 (tt0) REVERT: A 985 TYR cc_start: 0.8800 (m-80) cc_final: 0.8498 (m-80) REVERT: A 1003 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7938 (tt) REVERT: A 1010 LYS cc_start: 0.8478 (tttt) cc_final: 0.8106 (ttmm) REVERT: A 1028 LYS cc_start: 0.8395 (mttt) cc_final: 0.8156 (mtmm) REVERT: A 1091 GLN cc_start: 0.7955 (mt0) cc_final: 0.7517 (mt0) REVERT: A 1095 ASP cc_start: 0.7700 (m-30) cc_final: 0.7236 (m-30) REVERT: A 1105 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7913 (tpp80) REVERT: A 1116 SER cc_start: 0.8777 (t) cc_final: 0.8254 (p) REVERT: A 1179 LYS cc_start: 0.8614 (ttpt) cc_final: 0.8304 (ttmm) REVERT: A 1180 GLN cc_start: 0.7577 (pt0) cc_final: 0.7352 (pt0) REVERT: A 1200 LYS cc_start: 0.8763 (mttm) cc_final: 0.8542 (mttm) REVERT: C 53 ASN cc_start: 0.8367 (p0) cc_final: 0.8030 (p0) REVERT: C 74 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7975 (t80) REVERT: C 86 SER cc_start: 0.8536 (t) cc_final: 0.8250 (p) REVERT: C 128 SER cc_start: 0.8931 (p) cc_final: 0.8686 (m) REVERT: C 624 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8524 (mm) REVERT: C 649 TYR cc_start: 0.8751 (m-80) cc_final: 0.8338 (m-10) REVERT: C 711 PHE cc_start: 0.8316 (m-80) cc_final: 0.7908 (m-80) REVERT: C 845 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: C 862 MET cc_start: 0.7630 (mtt) cc_final: 0.7413 (mtp) REVERT: C 1001 GLN cc_start: 0.8804 (mt0) cc_final: 0.8543 (mt0) REVERT: C 1064 ARG cc_start: 0.8446 (ttm110) cc_final: 0.8240 (mmm-85) REVERT: C 1095 ASP cc_start: 0.8322 (t0) cc_final: 0.7889 (t0) REVERT: C 1173 LYS cc_start: 0.8358 (mtpp) cc_final: 0.8053 (mtpp) REVERT: C 1183 SER cc_start: 0.8387 (t) cc_final: 0.7701 (p) REVERT: C 1205 MET cc_start: 0.7873 (ptp) cc_final: 0.7637 (ptp) REVERT: C 1214 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8716 (mtpp) REVERT: B 41 ASP cc_start: 0.8179 (t0) cc_final: 0.7756 (t70) REVERT: B 105 LYS cc_start: 0.8093 (tttm) cc_final: 0.7628 (tttm) REVERT: B 147 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6766 (tm-30) REVERT: B 148 ILE cc_start: 0.8191 (mp) cc_final: 0.7866 (tt) REVERT: B 320 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7726 (ttm170) REVERT: B 467 PHE cc_start: 0.8511 (m-80) cc_final: 0.8294 (m-10) REVERT: B 667 TYR cc_start: 0.8293 (m-80) cc_final: 0.8084 (m-80) REVERT: B 702 ASN cc_start: 0.8067 (t0) cc_final: 0.7626 (t0) REVERT: B 729 TYR cc_start: 0.8307 (t80) cc_final: 0.7867 (t80) REVERT: B 745 ASP cc_start: 0.7929 (t0) cc_final: 0.7476 (t70) REVERT: B 746 TYR cc_start: 0.8334 (t80) cc_final: 0.8059 (t80) REVERT: B 878 ASP cc_start: 0.7946 (p0) cc_final: 0.7707 (p0) REVERT: B 883 ASP cc_start: 0.8407 (t0) cc_final: 0.8171 (t0) REVERT: B 912 LYS cc_start: 0.8536 (ptmt) cc_final: 0.8176 (ptmt) REVERT: B 999 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8280 (mtpt) REVERT: B 1038 GLN cc_start: 0.8471 (tp40) cc_final: 0.7723 (tp40) REVERT: B 1060 GLU cc_start: 0.8469 (tt0) cc_final: 0.8122 (tt0) REVERT: B 1064 ARG cc_start: 0.8931 (mtp180) cc_final: 0.8656 (mtp-110) REVERT: B 1090 SER cc_start: 0.8844 (t) cc_final: 0.8574 (m) REVERT: B 1095 ASP cc_start: 0.8033 (t0) cc_final: 0.7650 (t0) REVERT: B 1156 VAL cc_start: 0.8718 (p) cc_final: 0.8350 (m) REVERT: B 1212 PHE cc_start: 0.7482 (m-10) cc_final: 0.6609 (m-80) outliers start: 110 outliers final: 69 residues processed: 653 average time/residue: 0.4050 time to fit residues: 427.9226 Evaluate side-chains 630 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 557 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1183 SER Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 308 optimal weight: 10.0000 chunk 323 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 347 optimal weight: 0.0060 chunk 228 optimal weight: 0.9980 chunk 269 optimal weight: 5.9990 chunk 78 optimal weight: 0.0770 chunk 322 optimal weight: 2.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 413 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.166029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124209 restraints weight = 47093.126| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.76 r_work: 0.3366 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 30347 Z= 0.106 Angle : 0.532 11.024 41478 Z= 0.268 Chirality : 0.043 0.258 4755 Planarity : 0.004 0.047 5286 Dihedral : 4.512 57.935 4676 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.99 % Allowed : 13.74 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.03 (0.13), residues: 3749 helix: 1.50 (0.21), residues: 747 sheet: -0.17 (0.18), residues: 774 loop : -1.74 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 174 HIS 0.010 0.001 HIS A 465 PHE 0.025 0.001 PHE A 566 TYR 0.021 0.001 TYR A 699 ARG 0.007 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 25) link_NAG-ASN : angle 2.42764 ( 75) link_BETA1-4 : bond 0.00413 ( 4) link_BETA1-4 : angle 1.58181 ( 12) hydrogen bonds : bond 0.04071 ( 955) hydrogen bonds : angle 4.38471 ( 2683) SS BOND : bond 0.00347 ( 69) SS BOND : angle 1.64958 ( 138) covalent geometry : bond 0.00242 (30249) covalent geometry : angle 0.51342 (41253) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 566 time to evaluate : 4.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8526 (m-80) cc_final: 0.8311 (m-80) REVERT: A 234 HIS cc_start: 0.7669 (m90) cc_final: 0.7327 (m90) REVERT: A 238 MET cc_start: 0.6642 (ptp) cc_final: 0.6344 (ptp) REVERT: A 245 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7228 (pt) REVERT: A 323 ASN cc_start: 0.7292 (p0) cc_final: 0.7003 (p0) REVERT: A 357 SER cc_start: 0.8472 (t) cc_final: 0.8260 (p) REVERT: A 366 ASP cc_start: 0.7454 (t0) cc_final: 0.7115 (t0) REVERT: A 473 PHE cc_start: 0.8204 (t80) cc_final: 0.7668 (t80) REVERT: A 500 LYS cc_start: 0.8441 (ptpt) cc_final: 0.7950 (ptpt) REVERT: A 555 LYS cc_start: 0.8199 (tppp) cc_final: 0.7758 (tppp) REVERT: A 577 PHE cc_start: 0.7832 (m-80) cc_final: 0.7619 (m-10) REVERT: A 610 SER cc_start: 0.8812 (t) cc_final: 0.8213 (m) REVERT: A 632 ILE cc_start: 0.8559 (mt) cc_final: 0.8249 (mp) REVERT: A 635 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7371 (tm-30) REVERT: A 649 TYR cc_start: 0.7899 (m-10) cc_final: 0.7654 (m-10) REVERT: A 768 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7972 (mm-30) REVERT: A 806 SER cc_start: 0.8871 (m) cc_final: 0.8606 (t) REVERT: A 827 ASP cc_start: 0.7984 (m-30) cc_final: 0.7646 (m-30) REVERT: A 828 LEU cc_start: 0.8646 (mm) cc_final: 0.8396 (mt) REVERT: A 863 GLN cc_start: 0.8059 (tp40) cc_final: 0.7850 (tt0) REVERT: A 985 TYR cc_start: 0.8659 (m-80) cc_final: 0.8333 (m-80) REVERT: A 1003 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7771 (tt) REVERT: A 1010 LYS cc_start: 0.8300 (tttt) cc_final: 0.7926 (ttmm) REVERT: A 1091 GLN cc_start: 0.7635 (mt0) cc_final: 0.7338 (mm-40) REVERT: A 1095 ASP cc_start: 0.7527 (m-30) cc_final: 0.7031 (m-30) REVERT: A 1105 ARG cc_start: 0.8020 (tpp80) cc_final: 0.7675 (tpp80) REVERT: A 1116 SER cc_start: 0.8698 (t) cc_final: 0.8138 (p) REVERT: A 1179 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8292 (ptmt) REVERT: A 1180 GLN cc_start: 0.7345 (pt0) cc_final: 0.7049 (pt0) REVERT: C 53 ASN cc_start: 0.8252 (p0) cc_final: 0.7929 (p0) REVERT: C 74 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7777 (t80) REVERT: C 86 SER cc_start: 0.8382 (t) cc_final: 0.8149 (p) REVERT: C 128 SER cc_start: 0.8800 (p) cc_final: 0.8582 (m) REVERT: C 384 ASN cc_start: 0.8410 (m-40) cc_final: 0.8143 (m-40) REVERT: C 624 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8424 (mm) REVERT: C 649 TYR cc_start: 0.8509 (m-80) cc_final: 0.8172 (m-10) REVERT: C 683 GLN cc_start: 0.8475 (tp40) cc_final: 0.8257 (tp-100) REVERT: C 711 PHE cc_start: 0.8127 (m-80) cc_final: 0.7715 (m-80) REVERT: C 738 MET cc_start: 0.8665 (mmm) cc_final: 0.8166 (mmm) REVERT: C 845 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: C 981 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7921 (mp) REVERT: C 996 VAL cc_start: 0.8578 (p) cc_final: 0.8376 (m) REVERT: C 1064 ARG cc_start: 0.8259 (ttm110) cc_final: 0.8056 (mmm-85) REVERT: C 1095 ASP cc_start: 0.8115 (t0) cc_final: 0.7675 (t0) REVERT: C 1183 SER cc_start: 0.8310 (t) cc_final: 0.7620 (p) REVERT: C 1214 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8560 (mtpp) REVERT: B 41 ASP cc_start: 0.8028 (t0) cc_final: 0.7612 (t70) REVERT: B 147 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6435 (tm-30) REVERT: B 148 ILE cc_start: 0.7983 (mp) cc_final: 0.7667 (tt) REVERT: B 237 VAL cc_start: 0.7002 (OUTLIER) cc_final: 0.6784 (p) REVERT: B 289 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 320 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7560 (ttm170) REVERT: B 467 PHE cc_start: 0.8504 (m-80) cc_final: 0.8293 (m-10) REVERT: B 667 TYR cc_start: 0.8129 (m-80) cc_final: 0.7811 (m-80) REVERT: B 702 ASN cc_start: 0.7923 (t0) cc_final: 0.7373 (t0) REVERT: B 745 ASP cc_start: 0.7651 (t0) cc_final: 0.7167 (t70) REVERT: B 746 TYR cc_start: 0.8233 (t80) cc_final: 0.7962 (t80) REVERT: B 878 ASP cc_start: 0.7745 (p0) cc_final: 0.7444 (p0) REVERT: B 883 ASP cc_start: 0.8183 (t0) cc_final: 0.7935 (t0) REVERT: B 912 LYS cc_start: 0.8356 (ptmt) cc_final: 0.7975 (ptmt) REVERT: B 999 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8133 (mtpt) REVERT: B 1038 GLN cc_start: 0.8192 (tp40) cc_final: 0.7427 (tp40) REVERT: B 1060 GLU cc_start: 0.8162 (tt0) cc_final: 0.7909 (tt0) REVERT: B 1064 ARG cc_start: 0.8729 (mtp180) cc_final: 0.8483 (mtp85) REVERT: B 1091 GLN cc_start: 0.8435 (tt0) cc_final: 0.8201 (tt0) REVERT: B 1095 ASP cc_start: 0.7791 (t0) cc_final: 0.7412 (t0) REVERT: B 1156 VAL cc_start: 0.8681 (p) cc_final: 0.8307 (m) REVERT: B 1212 PHE cc_start: 0.7390 (m-10) cc_final: 0.6527 (m-80) outliers start: 98 outliers final: 75 residues processed: 620 average time/residue: 0.6464 time to fit residues: 661.6700 Evaluate side-chains 625 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 543 time to evaluate : 4.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1013 LEU Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 156 optimal weight: 0.6980 chunk 253 optimal weight: 4.9990 chunk 134 optimal weight: 30.0000 chunk 157 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 236 optimal weight: 0.6980 chunk 277 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.162497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121118 restraints weight = 46625.075| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.76 r_work: 0.3318 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 30347 Z= 0.198 Angle : 0.575 11.024 41478 Z= 0.295 Chirality : 0.046 0.294 4755 Planarity : 0.004 0.048 5286 Dihedral : 4.662 57.606 4676 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.54 % Allowed : 13.64 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.01 (0.13), residues: 3749 helix: 1.48 (0.20), residues: 752 sheet: -0.17 (0.18), residues: 768 loop : -1.72 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 174 HIS 0.010 0.001 HIS C1145 PHE 0.026 0.002 PHE B 658 TYR 0.026 0.002 TYR B 958 ARG 0.006 0.001 ARG B 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 25) link_NAG-ASN : angle 2.43655 ( 75) link_BETA1-4 : bond 0.00380 ( 4) link_BETA1-4 : angle 1.42985 ( 12) hydrogen bonds : bond 0.05293 ( 955) hydrogen bonds : angle 4.57839 ( 2683) SS BOND : bond 0.00344 ( 69) SS BOND : angle 1.60356 ( 138) covalent geometry : bond 0.00464 (30249) covalent geometry : angle 0.55922 (41253) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 569 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 SER cc_start: 0.8659 (p) cc_final: 0.8451 (m) REVERT: A 147 GLU cc_start: 0.8108 (tt0) cc_final: 0.7500 (tt0) REVERT: A 160 HIS cc_start: 0.7707 (p-80) cc_final: 0.7272 (p-80) REVERT: A 234 HIS cc_start: 0.7929 (m90) cc_final: 0.7663 (m90) REVERT: A 238 MET cc_start: 0.6983 (ptp) cc_final: 0.6440 (ptp) REVERT: A 323 ASN cc_start: 0.7595 (p0) cc_final: 0.7281 (p0) REVERT: A 357 SER cc_start: 0.8575 (t) cc_final: 0.8373 (p) REVERT: A 366 ASP cc_start: 0.7697 (t0) cc_final: 0.7340 (t0) REVERT: A 408 PHE cc_start: 0.8406 (m-10) cc_final: 0.7936 (m-80) REVERT: A 500 LYS cc_start: 0.8570 (ptpt) cc_final: 0.8125 (ptpt) REVERT: A 555 LYS cc_start: 0.8398 (tppp) cc_final: 0.7917 (tppp) REVERT: A 577 PHE cc_start: 0.8121 (m-80) cc_final: 0.7889 (m-10) REVERT: A 610 SER cc_start: 0.8904 (t) cc_final: 0.8333 (m) REVERT: A 632 ILE cc_start: 0.8695 (mt) cc_final: 0.8438 (mp) REVERT: A 635 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 649 TYR cc_start: 0.8119 (m-10) cc_final: 0.7859 (m-10) REVERT: A 667 TYR cc_start: 0.8509 (m-80) cc_final: 0.8300 (m-80) REVERT: A 673 TYR cc_start: 0.8452 (t80) cc_final: 0.8238 (t80) REVERT: A 768 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8278 (mm-30) REVERT: A 806 SER cc_start: 0.8941 (m) cc_final: 0.8705 (t) REVERT: A 815 SER cc_start: 0.8741 (p) cc_final: 0.8512 (m) REVERT: A 827 ASP cc_start: 0.8338 (m-30) cc_final: 0.8028 (m-30) REVERT: A 828 LEU cc_start: 0.8769 (mm) cc_final: 0.8532 (mt) REVERT: A 916 VAL cc_start: 0.8731 (p) cc_final: 0.8452 (t) REVERT: A 985 TYR cc_start: 0.8821 (m-80) cc_final: 0.8478 (m-80) REVERT: A 1028 LYS cc_start: 0.8454 (mttt) cc_final: 0.8155 (mtmm) REVERT: A 1091 GLN cc_start: 0.7989 (mt0) cc_final: 0.7580 (mt0) REVERT: A 1095 ASP cc_start: 0.7794 (m-30) cc_final: 0.7328 (m-30) REVERT: A 1105 ARG cc_start: 0.8387 (tpp80) cc_final: 0.7990 (tpp80) REVERT: A 1116 SER cc_start: 0.8771 (t) cc_final: 0.8224 (p) REVERT: A 1180 GLN cc_start: 0.7577 (pt0) cc_final: 0.7282 (pt0) REVERT: C 74 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8176 (t80) REVERT: C 86 SER cc_start: 0.8480 (t) cc_final: 0.8170 (p) REVERT: C 128 SER cc_start: 0.8921 (p) cc_final: 0.8692 (m) REVERT: C 155 MET cc_start: 0.8793 (mmt) cc_final: 0.8420 (mmp) REVERT: C 437 ASN cc_start: 0.7763 (p0) cc_final: 0.7241 (p0) REVERT: C 683 GLN cc_start: 0.8590 (tp40) cc_final: 0.8375 (tp-100) REVERT: C 711 PHE cc_start: 0.8359 (m-80) cc_final: 0.7993 (m-80) REVERT: C 845 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: C 981 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8154 (mp) REVERT: C 998 ASN cc_start: 0.8734 (t0) cc_final: 0.8443 (m110) REVERT: C 1095 ASP cc_start: 0.8371 (t0) cc_final: 0.7962 (t0) REVERT: C 1183 SER cc_start: 0.8412 (t) cc_final: 0.7729 (p) REVERT: C 1214 LYS cc_start: 0.8940 (mtpp) cc_final: 0.8699 (mtpp) REVERT: C 1218 ILE cc_start: 0.8810 (mt) cc_final: 0.8540 (mm) REVERT: B 41 ASP cc_start: 0.8287 (t0) cc_final: 0.7863 (t70) REVERT: B 105 LYS cc_start: 0.8027 (tttm) cc_final: 0.7599 (tttm) REVERT: B 147 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7018 (tm-30) REVERT: B 148 ILE cc_start: 0.8264 (mp) cc_final: 0.7888 (tt) REVERT: B 320 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7805 (mtt-85) REVERT: B 467 PHE cc_start: 0.8473 (m-80) cc_final: 0.8253 (m-10) REVERT: B 667 TYR cc_start: 0.8358 (m-80) cc_final: 0.8081 (m-80) REVERT: B 702 ASN cc_start: 0.8086 (t0) cc_final: 0.7636 (t0) REVERT: B 745 ASP cc_start: 0.7989 (t0) cc_final: 0.7581 (t70) REVERT: B 746 TYR cc_start: 0.8364 (t80) cc_final: 0.8129 (t80) REVERT: B 883 ASP cc_start: 0.8427 (t0) cc_final: 0.8213 (t0) REVERT: B 887 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8274 (pp) REVERT: B 912 LYS cc_start: 0.8590 (ptmt) cc_final: 0.8211 (ptmt) REVERT: B 999 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8276 (mtpt) REVERT: B 1038 GLN cc_start: 0.8494 (tp40) cc_final: 0.7744 (tp40) REVERT: B 1060 GLU cc_start: 0.8512 (tt0) cc_final: 0.8244 (tt0) REVERT: B 1095 ASP cc_start: 0.8054 (t0) cc_final: 0.7686 (t0) REVERT: B 1212 PHE cc_start: 0.7704 (m-10) cc_final: 0.6734 (m-80) outliers start: 116 outliers final: 82 residues processed: 630 average time/residue: 0.4117 time to fit residues: 420.5865 Evaluate side-chains 635 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 549 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1183 SER Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 345 optimal weight: 0.8980 chunk 275 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 311 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 330 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 307 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 535 GLN C 265 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 ASN B 152 GLN B 201 HIS B 351 ASN B1122 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.162515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120876 restraints weight = 46815.158| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.78 r_work: 0.3312 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30347 Z= 0.175 Angle : 0.573 11.949 41478 Z= 0.290 Chirality : 0.046 0.495 4755 Planarity : 0.004 0.048 5286 Dihedral : 4.676 57.110 4674 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.36 % Allowed : 14.16 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3749 helix: 1.62 (0.21), residues: 738 sheet: -0.10 (0.18), residues: 780 loop : -1.67 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 174 HIS 0.009 0.001 HIS C 201 PHE 0.026 0.002 PHE A 566 TYR 0.021 0.002 TYR C 49 ARG 0.008 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 25) link_NAG-ASN : angle 2.41272 ( 75) link_BETA1-4 : bond 0.00280 ( 4) link_BETA1-4 : angle 1.32982 ( 12) hydrogen bonds : bond 0.05029 ( 955) hydrogen bonds : angle 4.56518 ( 2683) SS BOND : bond 0.00378 ( 69) SS BOND : angle 1.77048 ( 138) covalent geometry : bond 0.00407 (30249) covalent geometry : angle 0.55563 (41253) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 556 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8462 (p) REVERT: A 104 SER cc_start: 0.8517 (p) cc_final: 0.8301 (m) REVERT: A 147 GLU cc_start: 0.7846 (tt0) cc_final: 0.7230 (tt0) REVERT: A 234 HIS cc_start: 0.7782 (m90) cc_final: 0.7474 (m90) REVERT: A 238 MET cc_start: 0.6913 (ptp) cc_final: 0.6308 (ptp) REVERT: A 323 ASN cc_start: 0.7520 (p0) cc_final: 0.7218 (p0) REVERT: A 366 ASP cc_start: 0.7456 (t0) cc_final: 0.7101 (t0) REVERT: A 408 PHE cc_start: 0.8269 (m-10) cc_final: 0.7836 (m-80) REVERT: A 448 TYR cc_start: 0.8400 (m-10) cc_final: 0.8118 (m-80) REVERT: A 500 LYS cc_start: 0.8500 (ptpt) cc_final: 0.8022 (ptpt) REVERT: A 555 LYS cc_start: 0.8241 (tppp) cc_final: 0.7754 (tppp) REVERT: A 577 PHE cc_start: 0.7825 (m-80) cc_final: 0.7574 (m-80) REVERT: A 632 ILE cc_start: 0.8608 (mt) cc_final: 0.8360 (mp) REVERT: A 635 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7432 (tm-30) REVERT: A 649 TYR cc_start: 0.7960 (m-10) cc_final: 0.7700 (m-10) REVERT: A 768 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7974 (mm-30) REVERT: A 806 SER cc_start: 0.8882 (m) cc_final: 0.8664 (t) REVERT: A 827 ASP cc_start: 0.8017 (m-30) cc_final: 0.7684 (m-30) REVERT: A 828 LEU cc_start: 0.8690 (mm) cc_final: 0.8444 (mt) REVERT: A 915 ASP cc_start: 0.6958 (t0) cc_final: 0.6745 (t0) REVERT: A 985 TYR cc_start: 0.8655 (m-80) cc_final: 0.8330 (m-80) REVERT: A 1028 LYS cc_start: 0.8291 (mttt) cc_final: 0.7944 (mtmm) REVERT: A 1091 GLN cc_start: 0.7727 (mt0) cc_final: 0.7325 (mt0) REVERT: A 1095 ASP cc_start: 0.7531 (m-30) cc_final: 0.7078 (m-30) REVERT: A 1105 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7748 (tpp80) REVERT: A 1116 SER cc_start: 0.8695 (t) cc_final: 0.8139 (p) REVERT: C 53 ASN cc_start: 0.8194 (p0) cc_final: 0.7926 (p0) REVERT: C 86 SER cc_start: 0.8392 (t) cc_final: 0.8085 (p) REVERT: C 128 SER cc_start: 0.8784 (p) cc_final: 0.8566 (m) REVERT: C 437 ASN cc_start: 0.7673 (p0) cc_final: 0.7237 (p0) REVERT: C 683 GLN cc_start: 0.8463 (tp40) cc_final: 0.8226 (tp-100) REVERT: C 711 PHE cc_start: 0.8183 (m-80) cc_final: 0.7844 (m-80) REVERT: C 845 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: C 981 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7995 (mp) REVERT: C 996 VAL cc_start: 0.8640 (p) cc_final: 0.8438 (m) REVERT: C 998 ASN cc_start: 0.8669 (t0) cc_final: 0.8413 (m-40) REVERT: C 1064 ARG cc_start: 0.8318 (ttm110) cc_final: 0.8015 (mtp-110) REVERT: C 1095 ASP cc_start: 0.8122 (t0) cc_final: 0.7721 (t0) REVERT: C 1183 SER cc_start: 0.8384 (t) cc_final: 0.7734 (p) REVERT: C 1214 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8576 (mtpp) REVERT: C 1218 ILE cc_start: 0.8793 (mt) cc_final: 0.8554 (mm) REVERT: B 41 ASP cc_start: 0.8084 (t0) cc_final: 0.7656 (t70) REVERT: B 75 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7620 (ptm160) REVERT: B 105 LYS cc_start: 0.7926 (tttm) cc_final: 0.7530 (tttm) REVERT: B 147 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6727 (tm-30) REVERT: B 148 ILE cc_start: 0.8089 (mp) cc_final: 0.7708 (tt) REVERT: B 320 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7444 (mtt-85) REVERT: B 348 ILE cc_start: 0.8810 (mt) cc_final: 0.8342 (tp) REVERT: B 398 ARG cc_start: 0.8370 (ptp-110) cc_final: 0.7944 (mtt-85) REVERT: B 467 PHE cc_start: 0.8466 (m-80) cc_final: 0.8231 (m-10) REVERT: B 667 TYR cc_start: 0.8233 (m-80) cc_final: 0.7909 (m-80) REVERT: B 702 ASN cc_start: 0.8001 (t0) cc_final: 0.7540 (t0) REVERT: B 745 ASP cc_start: 0.7734 (t0) cc_final: 0.7420 (t70) REVERT: B 746 TYR cc_start: 0.8275 (t80) cc_final: 0.8022 (t80) REVERT: B 883 ASP cc_start: 0.8195 (t0) cc_final: 0.7978 (t0) REVERT: B 887 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8253 (pp) REVERT: B 912 LYS cc_start: 0.8463 (ptmt) cc_final: 0.8104 (ptmt) REVERT: B 999 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8160 (mtpt) REVERT: B 1038 GLN cc_start: 0.8249 (tp40) cc_final: 0.7486 (tp40) REVERT: B 1060 GLU cc_start: 0.8218 (tt0) cc_final: 0.7943 (tt0) REVERT: B 1064 ARG cc_start: 0.8775 (mtp180) cc_final: 0.8525 (mtp85) REVERT: B 1095 ASP cc_start: 0.7813 (t0) cc_final: 0.7433 (t0) REVERT: B 1174 GLN cc_start: 0.8493 (tp40) cc_final: 0.8235 (mm-40) REVERT: B 1212 PHE cc_start: 0.7668 (m-10) cc_final: 0.6703 (m-80) outliers start: 110 outliers final: 83 residues processed: 614 average time/residue: 0.3894 time to fit residues: 385.2613 Evaluate side-chains 624 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 537 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 884 PHE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1183 SER Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 101 optimal weight: 0.9990 chunk 291 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 344 optimal weight: 0.4980 chunk 278 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 169 optimal weight: 0.0050 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN A 465 HIS ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 998 ASN B1117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.163555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122396 restraints weight = 46904.980| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.73 r_work: 0.3340 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30347 Z= 0.114 Angle : 0.534 11.737 41478 Z= 0.270 Chirality : 0.044 0.408 4755 Planarity : 0.004 0.045 5286 Dihedral : 4.455 57.337 4674 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.11 % Allowed : 15.02 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3749 helix: 1.83 (0.21), residues: 733 sheet: 0.01 (0.18), residues: 771 loop : -1.59 (0.12), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 174 HIS 0.008 0.001 HIS C 201 PHE 0.026 0.001 PHE A 566 TYR 0.023 0.001 TYR C 649 ARG 0.006 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 25) link_NAG-ASN : angle 2.15109 ( 75) link_BETA1-4 : bond 0.00474 ( 4) link_BETA1-4 : angle 1.30911 ( 12) hydrogen bonds : bond 0.04311 ( 955) hydrogen bonds : angle 4.44572 ( 2683) SS BOND : bond 0.00290 ( 69) SS BOND : angle 1.48117 ( 138) covalent geometry : bond 0.00260 (30249) covalent geometry : angle 0.52039 (41253) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 545 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8617 (mt) cc_final: 0.8241 (mm) REVERT: A 234 HIS cc_start: 0.7972 (m90) cc_final: 0.7696 (m90) REVERT: A 238 MET cc_start: 0.7169 (ptp) cc_final: 0.6613 (ptp) REVERT: A 323 ASN cc_start: 0.7708 (p0) cc_final: 0.7415 (p0) REVERT: A 366 ASP cc_start: 0.7693 (t0) cc_final: 0.7322 (t0) REVERT: A 408 PHE cc_start: 0.8445 (m-10) cc_final: 0.8060 (m-80) REVERT: A 448 TYR cc_start: 0.8509 (m-10) cc_final: 0.8262 (m-80) REVERT: A 500 LYS cc_start: 0.8603 (ptpt) cc_final: 0.8170 (ptpt) REVERT: A 555 LYS cc_start: 0.8353 (tppp) cc_final: 0.7839 (tppp) REVERT: A 632 ILE cc_start: 0.8697 (mt) cc_final: 0.8434 (mp) REVERT: A 635 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7671 (tm-30) REVERT: A 649 TYR cc_start: 0.8046 (m-10) cc_final: 0.7833 (m-10) REVERT: A 673 TYR cc_start: 0.8445 (t80) cc_final: 0.8229 (t80) REVERT: A 768 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8300 (mm-30) REVERT: A 806 SER cc_start: 0.8941 (m) cc_final: 0.8701 (t) REVERT: A 827 ASP cc_start: 0.8322 (m-30) cc_final: 0.8008 (m-30) REVERT: A 828 LEU cc_start: 0.8761 (mm) cc_final: 0.8512 (mt) REVERT: A 915 ASP cc_start: 0.7147 (t0) cc_final: 0.6899 (t0) REVERT: A 985 TYR cc_start: 0.8798 (m-80) cc_final: 0.8461 (m-80) REVERT: A 1028 LYS cc_start: 0.8383 (mttt) cc_final: 0.8084 (mtmm) REVERT: A 1091 GLN cc_start: 0.7958 (mt0) cc_final: 0.7638 (mm-40) REVERT: A 1095 ASP cc_start: 0.7801 (m-30) cc_final: 0.7334 (m-30) REVERT: A 1105 ARG cc_start: 0.8367 (tpp80) cc_final: 0.7984 (tpp80) REVERT: A 1116 SER cc_start: 0.8770 (t) cc_final: 0.8237 (p) REVERT: A 1193 TYR cc_start: 0.8871 (t80) cc_final: 0.8381 (t80) REVERT: C 53 ASN cc_start: 0.8291 (p0) cc_final: 0.7996 (p0) REVERT: C 74 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7893 (t80) REVERT: C 86 SER cc_start: 0.8487 (t) cc_final: 0.8137 (p) REVERT: C 128 SER cc_start: 0.8899 (p) cc_final: 0.8653 (m) REVERT: C 155 MET cc_start: 0.8783 (mmt) cc_final: 0.8443 (mmp) REVERT: C 635 GLU cc_start: 0.8076 (tp30) cc_final: 0.7843 (tp30) REVERT: C 700 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.7974 (p) REVERT: C 711 PHE cc_start: 0.8310 (m-80) cc_final: 0.8061 (m-10) REVERT: C 763 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8345 (mtm110) REVERT: C 845 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: C 981 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8125 (mp) REVERT: C 996 VAL cc_start: 0.8714 (p) cc_final: 0.8503 (m) REVERT: C 1064 ARG cc_start: 0.8417 (ttm110) cc_final: 0.8140 (mtp-110) REVERT: C 1095 ASP cc_start: 0.8402 (t0) cc_final: 0.8000 (t0) REVERT: C 1214 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8686 (mtpp) REVERT: B 41 ASP cc_start: 0.8334 (t0) cc_final: 0.7908 (t70) REVERT: B 105 LYS cc_start: 0.8043 (tttm) cc_final: 0.7635 (tttm) REVERT: B 147 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7079 (tm-30) REVERT: B 148 ILE cc_start: 0.8276 (mp) cc_final: 0.7870 (tt) REVERT: B 320 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7730 (mtt-85) REVERT: B 348 ILE cc_start: 0.8905 (mt) cc_final: 0.8439 (tp) REVERT: B 467 PHE cc_start: 0.8422 (m-80) cc_final: 0.8207 (m-10) REVERT: B 702 ASN cc_start: 0.8116 (t0) cc_final: 0.7728 (t0) REVERT: B 745 ASP cc_start: 0.7957 (t0) cc_final: 0.7528 (t70) REVERT: B 746 TYR cc_start: 0.8349 (t80) cc_final: 0.8132 (t80) REVERT: B 883 ASP cc_start: 0.8454 (t0) cc_final: 0.8234 (t0) REVERT: B 912 LYS cc_start: 0.8596 (ptmt) cc_final: 0.8232 (ptmt) REVERT: B 999 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8298 (mtpt) REVERT: B 1038 GLN cc_start: 0.8510 (tp40) cc_final: 0.7771 (tp40) REVERT: B 1060 GLU cc_start: 0.8528 (tt0) cc_final: 0.8258 (tt0) REVERT: B 1064 ARG cc_start: 0.8901 (mtp180) cc_final: 0.8642 (mtp85) REVERT: B 1174 GLN cc_start: 0.8611 (tp40) cc_final: 0.8364 (mm-40) REVERT: B 1212 PHE cc_start: 0.7791 (m-10) cc_final: 0.6842 (m-80) outliers start: 102 outliers final: 79 residues processed: 601 average time/residue: 0.3990 time to fit residues: 383.8630 Evaluate side-chains 622 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 539 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1183 SER Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 3.9990 chunk 345 optimal weight: 0.3980 chunk 124 optimal weight: 50.0000 chunk 158 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 353 optimal weight: 2.9990 chunk 303 optimal weight: 20.0000 chunk 267 optimal weight: 3.9990 chunk 285 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 321 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN C 353 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 ASN B 821 ASN B 998 ASN B1117 GLN B1122 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.161405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119805 restraints weight = 46859.167| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.75 r_work: 0.3302 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30347 Z= 0.205 Angle : 0.593 11.899 41478 Z= 0.302 Chirality : 0.046 0.367 4755 Planarity : 0.004 0.050 5286 Dihedral : 4.703 57.075 4674 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.51 % Allowed : 14.90 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3749 helix: 1.68 (0.20), residues: 739 sheet: -0.05 (0.18), residues: 785 loop : -1.61 (0.12), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.009 0.001 HIS C1145 PHE 0.026 0.002 PHE A 566 TYR 0.033 0.002 TYR C 649 ARG 0.011 0.001 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 25) link_NAG-ASN : angle 2.31297 ( 75) link_BETA1-4 : bond 0.00324 ( 4) link_BETA1-4 : angle 1.35480 ( 12) hydrogen bonds : bond 0.05380 ( 955) hydrogen bonds : angle 4.60179 ( 2683) SS BOND : bond 0.00450 ( 69) SS BOND : angle 1.60826 ( 138) covalent geometry : bond 0.00479 (30249) covalent geometry : angle 0.57827 (41253) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 542 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8111 (tt0) cc_final: 0.7469 (tt0) REVERT: A 232 LEU cc_start: 0.8744 (mt) cc_final: 0.8324 (mm) REVERT: A 238 MET cc_start: 0.7202 (ptp) cc_final: 0.6868 (ptp) REVERT: A 323 ASN cc_start: 0.7802 (p0) cc_final: 0.7510 (p0) REVERT: A 366 ASP cc_start: 0.7721 (t0) cc_final: 0.7343 (t0) REVERT: A 378 ILE cc_start: 0.8461 (pt) cc_final: 0.8222 (pt) REVERT: A 408 PHE cc_start: 0.8476 (m-10) cc_final: 0.7987 (m-80) REVERT: A 448 TYR cc_start: 0.8637 (m-10) cc_final: 0.8229 (m-80) REVERT: A 500 LYS cc_start: 0.8621 (ptpt) cc_final: 0.8175 (ptpt) REVERT: A 555 LYS cc_start: 0.8388 (tppp) cc_final: 0.7879 (tppp) REVERT: A 577 PHE cc_start: 0.8029 (m-80) cc_final: 0.7766 (m-10) REVERT: A 632 ILE cc_start: 0.8724 (mt) cc_final: 0.8479 (mp) REVERT: A 649 TYR cc_start: 0.8127 (m-10) cc_final: 0.7856 (m-10) REVERT: A 673 TYR cc_start: 0.8480 (t80) cc_final: 0.8260 (t80) REVERT: A 768 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8350 (mm-30) REVERT: A 806 SER cc_start: 0.8958 (m) cc_final: 0.8739 (t) REVERT: A 827 ASP cc_start: 0.8320 (m-30) cc_final: 0.7994 (m-30) REVERT: A 828 LEU cc_start: 0.8769 (mm) cc_final: 0.8509 (mt) REVERT: A 915 ASP cc_start: 0.7242 (t0) cc_final: 0.7014 (t0) REVERT: A 985 TYR cc_start: 0.8811 (m-80) cc_final: 0.8461 (m-80) REVERT: A 1028 LYS cc_start: 0.8480 (mttt) cc_final: 0.8171 (mtpp) REVERT: A 1091 GLN cc_start: 0.8035 (mt0) cc_final: 0.7656 (mt0) REVERT: A 1095 ASP cc_start: 0.7835 (m-30) cc_final: 0.7377 (m-30) REVERT: A 1100 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7845 (tmtt) REVERT: A 1116 SER cc_start: 0.8775 (t) cc_final: 0.8231 (p) REVERT: C 53 ASN cc_start: 0.8367 (p0) cc_final: 0.8060 (p0) REVERT: C 74 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7973 (t80) REVERT: C 86 SER cc_start: 0.8518 (t) cc_final: 0.8171 (p) REVERT: C 128 SER cc_start: 0.8893 (p) cc_final: 0.8663 (m) REVERT: C 683 GLN cc_start: 0.8530 (tp40) cc_final: 0.8326 (tp-100) REVERT: C 711 PHE cc_start: 0.8379 (m-80) cc_final: 0.7992 (m-80) REVERT: C 845 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: C 981 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8163 (mp) REVERT: C 992 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8511 (t) REVERT: C 1064 ARG cc_start: 0.8453 (ttm110) cc_final: 0.8148 (mtp-110) REVERT: C 1095 ASP cc_start: 0.8381 (t0) cc_final: 0.7982 (t0) REVERT: C 1167 ASP cc_start: 0.8301 (m-30) cc_final: 0.8082 (m-30) REVERT: C 1173 LYS cc_start: 0.8341 (mtpp) cc_final: 0.8073 (mtpp) REVERT: C 1214 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8680 (mtpp) REVERT: B 105 LYS cc_start: 0.8041 (tttm) cc_final: 0.7635 (tttm) REVERT: B 148 ILE cc_start: 0.8315 (mp) cc_final: 0.7901 (tt) REVERT: B 320 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7817 (mtt-85) REVERT: B 348 ILE cc_start: 0.8914 (mt) cc_final: 0.8449 (tp) REVERT: B 398 ARG cc_start: 0.8305 (ptp-110) cc_final: 0.7975 (mtt-85) REVERT: B 467 PHE cc_start: 0.8402 (m-80) cc_final: 0.8161 (m-10) REVERT: B 667 TYR cc_start: 0.8416 (m-80) cc_final: 0.8118 (m-80) REVERT: B 702 ASN cc_start: 0.8220 (t0) cc_final: 0.7874 (t0) REVERT: B 813 ASP cc_start: 0.8362 (t0) cc_final: 0.8135 (t0) REVERT: B 912 LYS cc_start: 0.8682 (ptmt) cc_final: 0.8318 (ptmt) REVERT: B 999 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8319 (mtpt) REVERT: B 1038 GLN cc_start: 0.8510 (tp40) cc_final: 0.7782 (tp40) REVERT: B 1060 GLU cc_start: 0.8559 (tt0) cc_final: 0.8277 (tt0) REVERT: B 1174 GLN cc_start: 0.8640 (tp40) cc_final: 0.8383 (mm-40) outliers start: 115 outliers final: 96 residues processed: 605 average time/residue: 0.3999 time to fit residues: 390.6581 Evaluate side-chains 633 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 532 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 992 VAL Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1183 SER Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 227 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 243 optimal weight: 0.7980 chunk 185 optimal weight: 40.0000 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 342 optimal weight: 0.9980 chunk 338 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN B 998 ASN B1117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.162521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121561 restraints weight = 46626.929| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.62 r_work: 0.3330 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30347 Z= 0.136 Angle : 0.568 12.393 41478 Z= 0.287 Chirality : 0.045 0.350 4755 Planarity : 0.004 0.046 5286 Dihedral : 4.569 56.952 4674 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.96 % Allowed : 15.60 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3749 helix: 1.79 (0.21), residues: 734 sheet: 0.01 (0.18), residues: 780 loop : -1.57 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.007 0.001 HIS C 201 PHE 0.028 0.001 PHE A 566 TYR 0.035 0.001 TYR C 649 ARG 0.007 0.000 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 25) link_NAG-ASN : angle 2.27786 ( 75) link_BETA1-4 : bond 0.00446 ( 4) link_BETA1-4 : angle 1.27781 ( 12) hydrogen bonds : bond 0.04733 ( 955) hydrogen bonds : angle 4.50719 ( 2683) SS BOND : bond 0.00295 ( 69) SS BOND : angle 1.50540 ( 138) covalent geometry : bond 0.00313 (30249) covalent geometry : angle 0.55369 (41253) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 526 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8709 (mt) cc_final: 0.8283 (mm) REVERT: A 238 MET cc_start: 0.7096 (ptp) cc_final: 0.6820 (ptp) REVERT: A 323 ASN cc_start: 0.7777 (p0) cc_final: 0.7497 (p0) REVERT: A 366 ASP cc_start: 0.7680 (t0) cc_final: 0.7294 (t0) REVERT: A 408 PHE cc_start: 0.8411 (m-10) cc_final: 0.7981 (m-80) REVERT: A 448 TYR cc_start: 0.8622 (m-10) cc_final: 0.8252 (m-80) REVERT: A 500 LYS cc_start: 0.8589 (ptpt) cc_final: 0.8128 (ptpt) REVERT: A 555 LYS cc_start: 0.8365 (tppp) cc_final: 0.7861 (tppp) REVERT: A 632 ILE cc_start: 0.8672 (mt) cc_final: 0.8406 (mp) REVERT: A 649 TYR cc_start: 0.8067 (m-10) cc_final: 0.7833 (m-10) REVERT: A 768 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8266 (mm-30) REVERT: A 806 SER cc_start: 0.8936 (m) cc_final: 0.8704 (t) REVERT: A 827 ASP cc_start: 0.8270 (m-30) cc_final: 0.7935 (m-30) REVERT: A 828 LEU cc_start: 0.8715 (mm) cc_final: 0.8471 (mt) REVERT: A 915 ASP cc_start: 0.7171 (t0) cc_final: 0.6930 (t0) REVERT: A 985 TYR cc_start: 0.8753 (m-80) cc_final: 0.8397 (m-80) REVERT: A 1028 LYS cc_start: 0.8381 (mttt) cc_final: 0.8072 (mtpp) REVERT: A 1091 GLN cc_start: 0.7972 (mt0) cc_final: 0.7589 (mt0) REVERT: A 1095 ASP cc_start: 0.7782 (m-30) cc_final: 0.7329 (m-30) REVERT: A 1100 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7787 (tmtt) REVERT: A 1105 ARG cc_start: 0.8356 (tpp80) cc_final: 0.7966 (tpp80) REVERT: A 1116 SER cc_start: 0.8772 (t) cc_final: 0.8212 (p) REVERT: C 53 ASN cc_start: 0.8300 (p0) cc_final: 0.8040 (p0) REVERT: C 74 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7841 (t80) REVERT: C 120 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 128 SER cc_start: 0.8897 (p) cc_final: 0.8661 (m) REVERT: C 324 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8830 (mp) REVERT: C 635 GLU cc_start: 0.8071 (tp30) cc_final: 0.7837 (tp30) REVERT: C 683 GLN cc_start: 0.8516 (tp40) cc_final: 0.8308 (tp-100) REVERT: C 711 PHE cc_start: 0.8320 (m-80) cc_final: 0.8067 (m-10) REVERT: C 763 ARG cc_start: 0.8619 (mtm-85) cc_final: 0.8279 (mtm110) REVERT: C 845 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: C 981 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8076 (mp) REVERT: C 1064 ARG cc_start: 0.8415 (ttm110) cc_final: 0.8115 (mtp-110) REVERT: C 1095 ASP cc_start: 0.8344 (t0) cc_final: 0.7948 (t0) REVERT: C 1167 ASP cc_start: 0.8252 (m-30) cc_final: 0.8024 (m-30) REVERT: C 1173 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8052 (mtpp) REVERT: C 1214 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8657 (mtpp) REVERT: B 41 ASP cc_start: 0.8174 (t0) cc_final: 0.7781 (t70) REVERT: B 148 ILE cc_start: 0.8276 (mp) cc_final: 0.7865 (tt) REVERT: B 320 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7665 (mtt-85) REVERT: B 348 ILE cc_start: 0.8857 (mt) cc_final: 0.8383 (tp) REVERT: B 398 ARG cc_start: 0.8318 (ptp-110) cc_final: 0.7965 (mtt-85) REVERT: B 467 PHE cc_start: 0.8382 (m-80) cc_final: 0.8144 (m-10) REVERT: B 702 ASN cc_start: 0.8149 (t0) cc_final: 0.7810 (t0) REVERT: B 745 ASP cc_start: 0.8025 (t0) cc_final: 0.7586 (t70) REVERT: B 912 LYS cc_start: 0.8602 (ptmt) cc_final: 0.8222 (ptmt) REVERT: B 999 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8160 (mtpt) REVERT: B 1038 GLN cc_start: 0.8447 (tp40) cc_final: 0.7698 (tp40) REVERT: B 1060 GLU cc_start: 0.8514 (tt0) cc_final: 0.8216 (tt0) REVERT: B 1174 GLN cc_start: 0.8607 (tp40) cc_final: 0.8345 (mm-40) outliers start: 97 outliers final: 81 residues processed: 583 average time/residue: 0.3852 time to fit residues: 361.2723 Evaluate side-chains 603 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 517 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1183 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 158 optimal weight: 1.9990 chunk 181 optimal weight: 8.9990 chunk 213 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 337 optimal weight: 0.0470 chunk 153 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 chunk 144 optimal weight: 0.8980 chunk 368 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1206 ASN B 53 ASN B 998 ASN B1122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.163211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121862 restraints weight = 46832.195| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.72 r_work: 0.3328 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30347 Z= 0.121 Angle : 0.559 12.178 41478 Z= 0.282 Chirality : 0.044 0.342 4755 Planarity : 0.004 0.045 5286 Dihedral : 4.478 57.170 4674 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.96 % Allowed : 15.75 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3749 helix: 1.87 (0.21), residues: 733 sheet: 0.05 (0.18), residues: 772 loop : -1.55 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.007 0.001 HIS C 201 PHE 0.029 0.001 PHE A 566 TYR 0.049 0.001 TYR C 649 ARG 0.008 0.000 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 25) link_NAG-ASN : angle 2.24744 ( 75) link_BETA1-4 : bond 0.00488 ( 4) link_BETA1-4 : angle 1.28764 ( 12) hydrogen bonds : bond 0.04397 ( 955) hydrogen bonds : angle 4.42394 ( 2683) SS BOND : bond 0.00288 ( 69) SS BOND : angle 1.41722 ( 138) covalent geometry : bond 0.00277 (30249) covalent geometry : angle 0.54526 (41253) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 528 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 HIS cc_start: 0.7681 (p-80) cc_final: 0.7221 (p-80) REVERT: A 232 LEU cc_start: 0.8726 (mt) cc_final: 0.8321 (mm) REVERT: A 238 MET cc_start: 0.7138 (ptp) cc_final: 0.6837 (ptp) REVERT: A 323 ASN cc_start: 0.7809 (p0) cc_final: 0.7525 (p0) REVERT: A 366 ASP cc_start: 0.7696 (t0) cc_final: 0.7289 (t0) REVERT: A 408 PHE cc_start: 0.8380 (m-10) cc_final: 0.7995 (m-80) REVERT: A 448 TYR cc_start: 0.8621 (m-10) cc_final: 0.8275 (m-80) REVERT: A 464 ASP cc_start: 0.8375 (t0) cc_final: 0.7536 (t70) REVERT: A 473 PHE cc_start: 0.8214 (t80) cc_final: 0.8000 (t80) REVERT: A 555 LYS cc_start: 0.8375 (tppp) cc_final: 0.7839 (tppp) REVERT: A 632 ILE cc_start: 0.8668 (mt) cc_final: 0.8397 (mp) REVERT: A 768 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8293 (mm-30) REVERT: A 806 SER cc_start: 0.8928 (m) cc_final: 0.8683 (t) REVERT: A 827 ASP cc_start: 0.8277 (m-30) cc_final: 0.7930 (m-30) REVERT: A 828 LEU cc_start: 0.8734 (mm) cc_final: 0.8480 (mt) REVERT: A 985 TYR cc_start: 0.8767 (m-80) cc_final: 0.8402 (m-80) REVERT: A 1028 LYS cc_start: 0.8351 (mttt) cc_final: 0.8061 (mtpp) REVERT: A 1091 GLN cc_start: 0.7967 (mt0) cc_final: 0.7626 (mm-40) REVERT: A 1095 ASP cc_start: 0.7799 (m-30) cc_final: 0.7333 (m-30) REVERT: A 1100 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7809 (tmtt) REVERT: A 1105 ARG cc_start: 0.8333 (tpp80) cc_final: 0.7951 (tpp80) REVERT: A 1116 SER cc_start: 0.8781 (t) cc_final: 0.8230 (p) REVERT: A 1122 ASN cc_start: 0.8642 (m110) cc_final: 0.8405 (m110) REVERT: C 53 ASN cc_start: 0.8310 (p0) cc_final: 0.8049 (p0) REVERT: C 120 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7789 (mt-10) REVERT: C 128 SER cc_start: 0.8909 (p) cc_final: 0.8662 (m) REVERT: C 269 ASN cc_start: 0.8669 (t0) cc_final: 0.8442 (t0) REVERT: C 324 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8810 (mp) REVERT: C 425 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5793 (tt) REVERT: C 635 GLU cc_start: 0.8090 (tp30) cc_final: 0.7859 (tp30) REVERT: C 649 TYR cc_start: 0.8170 (m-10) cc_final: 0.7927 (m-80) REVERT: C 683 GLN cc_start: 0.8533 (tp40) cc_final: 0.8325 (tp-100) REVERT: C 711 PHE cc_start: 0.8316 (m-80) cc_final: 0.8066 (m-10) REVERT: C 763 ARG cc_start: 0.8630 (mtm-85) cc_final: 0.8287 (mtm110) REVERT: C 845 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: C 981 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8109 (mp) REVERT: C 1064 ARG cc_start: 0.8417 (ttm110) cc_final: 0.8123 (mtp-110) REVERT: C 1095 ASP cc_start: 0.8379 (t0) cc_final: 0.7975 (t0) REVERT: C 1167 ASP cc_start: 0.8281 (m-30) cc_final: 0.8055 (m-30) REVERT: C 1173 LYS cc_start: 0.8314 (mtpp) cc_final: 0.8097 (mtpp) REVERT: C 1214 LYS cc_start: 0.8905 (mtpp) cc_final: 0.8659 (mtpp) REVERT: B 41 ASP cc_start: 0.8181 (t0) cc_final: 0.7786 (t70) REVERT: B 105 LYS cc_start: 0.7939 (tttm) cc_final: 0.7610 (tttt) REVERT: B 148 ILE cc_start: 0.8332 (mp) cc_final: 0.7857 (tt) REVERT: B 320 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7701 (mtt-85) REVERT: B 326 ASP cc_start: 0.6723 (t70) cc_final: 0.6237 (t70) REVERT: B 348 ILE cc_start: 0.8883 (mt) cc_final: 0.8408 (tp) REVERT: B 398 ARG cc_start: 0.8295 (ptp-110) cc_final: 0.7953 (mtt-85) REVERT: B 467 PHE cc_start: 0.8384 (m-80) cc_final: 0.8138 (m-10) REVERT: B 702 ASN cc_start: 0.8141 (t0) cc_final: 0.7787 (t0) REVERT: B 729 TYR cc_start: 0.8363 (t80) cc_final: 0.7938 (t80) REVERT: B 745 ASP cc_start: 0.8033 (t0) cc_final: 0.7588 (t70) REVERT: B 912 LYS cc_start: 0.8597 (ptmt) cc_final: 0.8229 (ptmt) REVERT: B 999 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8216 (mtpt) REVERT: B 1038 GLN cc_start: 0.8467 (tp40) cc_final: 0.7728 (tp40) REVERT: B 1060 GLU cc_start: 0.8537 (tt0) cc_final: 0.8234 (tt0) REVERT: B 1174 GLN cc_start: 0.8628 (tp40) cc_final: 0.8374 (mm-40) outliers start: 97 outliers final: 81 residues processed: 585 average time/residue: 0.3939 time to fit residues: 372.2484 Evaluate side-chains 616 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 530 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1183 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 162 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 280 optimal weight: 0.0030 chunk 118 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 73 optimal weight: 0.0070 chunk 110 optimal weight: 0.9990 chunk 303 optimal weight: 0.0010 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 894 GLN ** 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 = 0.4044 r_free = 0.4044 target = 0.164382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123261 restraints weight = 46792.137| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.75 r_work: 0.3344 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30347 Z= 0.102 Angle : 0.544 11.816 41478 Z= 0.275 Chirality : 0.044 0.335 4755 Planarity : 0.004 0.046 5286 Dihedral : 4.392 57.369 4674 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.69 % Allowed : 15.78 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3749 helix: 1.95 (0.21), residues: 735 sheet: 0.07 (0.18), residues: 786 loop : -1.51 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.007 0.001 HIS C 201 PHE 0.035 0.001 PHE A 566 TYR 0.017 0.001 TYR A 699 ARG 0.007 0.000 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 25) link_NAG-ASN : angle 2.16165 ( 75) link_BETA1-4 : bond 0.00474 ( 4) link_BETA1-4 : angle 1.25523 ( 12) hydrogen bonds : bond 0.03953 ( 955) hydrogen bonds : angle 4.37435 ( 2683) SS BOND : bond 0.00267 ( 69) SS BOND : angle 1.43587 ( 138) covalent geometry : bond 0.00229 (30249) covalent geometry : angle 0.53092 (41253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23727.33 seconds wall clock time: 411 minutes 42.65 seconds (24702.65 seconds total)