Starting phenix.real_space_refine on Sat Feb 7 11:11:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o81_70214/02_2026/9o81_70214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o81_70214/02_2026/9o81_70214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o81_70214/02_2026/9o81_70214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o81_70214/02_2026/9o81_70214.map" model { file = "/net/cci-nas-00/data/ceres_data/9o81_70214/02_2026/9o81_70214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o81_70214/02_2026/9o81_70214.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 222 5.16 5 C 20606 2.51 5 N 5304 2.21 5 O 5544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31676 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7863 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 991} Chain breaks: 8 Unresolved non-hydrogen bonds: 542 Unresolved non-hydrogen angles: 668 Unresolved non-hydrogen dihedrals: 462 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 17, 'ARG:plan': 15, 'ASP:plan': 9, 'HIS:plan': 6, 'GLN:plan1': 14, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 325 Chain: "B" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7835 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 990} Chain breaks: 8 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 482 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'TRP:plan': 4, 'GLU:plan': 16, 'ARG:plan': 12, 'ASP:plan': 8, 'HIS:plan': 6, 'GLN:plan1': 12, 'ASN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 307 Chain: "A" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7818 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 995} Chain breaks: 6 Unresolved non-hydrogen bonds: 605 Unresolved non-hydrogen angles: 738 Unresolved non-hydrogen dihedrals: 503 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 11, 'HIS:plan': 5, 'GLN:plan1': 14, 'TRP:plan': 1, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 363 Chain: "D" Number of atoms: 7740 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1039, 7730 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 997} Chain breaks: 6 Unresolved non-hydrogen bonds: 722 Unresolved non-hydrogen angles: 889 Unresolved non-hydrogen dihedrals: 600 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 23, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 14, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 6, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 443 Conformer: "B" Number of residues, atoms: 1039, 7730 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 997} Chain breaks: 6 Unresolved non-hydrogen bonds: 722 Unresolved non-hydrogen angles: 889 Unresolved non-hydrogen dihedrals: 600 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 23, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 14, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 6, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 443 bond proxies already assigned to first conformer: 7896 Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS D 674 " occ=0.37 ... (18 atoms not shown) pdb=" NE2BHIS D 674 " occ=0.63 Time building chain proxies: 8.92, per 1000 atoms: 0.28 Number of scatterers: 31676 At special positions: 0 Unit cell: (155.288, 155.288, 160.244, 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 222 16.00 O 5544 8.00 N 5304 7.00 C 20606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C1044 " - pdb=" SG CYS C1061 " distance=2.04 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1061 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1061 " distance=2.04 Simple disulfide: pdb=" SG CYS D1044 " - pdb=" SG CYS D1061 " distance=2.04 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 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7816 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 12 sheets defined 64.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 163 through 181 removed outlier: 3.918A pdb=" N ILE C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 206 removed outlier: 3.619A pdb=" N HIS C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.693A pdb=" N GLN C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.671A pdb=" N SER C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 removed outlier: 3.508A pdb=" N ILE C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 365 Processing helix chain 'C' and resid 371 through 387 Processing helix chain 'C' and resid 404 through 418 removed outlier: 4.020A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 431 Processing helix chain 'C' and resid 433 through 440 removed outlier: 3.825A pdb=" N ALA C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 464 Processing helix chain 'C' and resid 465 through 476 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 501 through 512 Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 555 through 565 removed outlier: 3.507A pdb=" N LEU C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 625 removed outlier: 3.980A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.583A pdb=" N HIS C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 661 Processing helix chain 'C' and resid 665 through 694 removed outlier: 3.946A pdb=" N SER C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 702 Processing helix chain 'C' and resid 706 through 710 removed outlier: 3.727A pdb=" N SER C 710 " --> pdb=" O LYS C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 723 through 729 Processing helix chain 'C' and resid 729 through 742 Processing helix chain 'C' and resid 749 through 760 removed outlier: 3.680A pdb=" N LEU C 759 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 760 " --> pdb=" O LEU C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 767 removed outlier: 3.765A pdb=" N ILE C 764 " --> pdb=" O PRO C 761 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 845 Processing helix chain 'C' and resid 847 through 871 Processing helix chain 'C' and resid 879 through 902 Processing helix chain 'C' and resid 907 through 918 removed outlier: 4.431A pdb=" N GLU C 918 " --> pdb=" O VAL C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 939 removed outlier: 3.587A pdb=" N VAL C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 967 removed outlier: 3.994A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 958 " --> pdb=" O VAL C 954 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU C 963 " --> pdb=" O TRP C 959 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU C 964 " --> pdb=" O TYR C 960 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP C 965 " --> pdb=" O ILE C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 1010 removed outlier: 4.529A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C1010 " --> pdb=" O GLN C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1024 removed outlier: 3.582A pdb=" N LYS C1021 " --> pdb=" O TRP C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1033 removed outlier: 3.536A pdb=" N ILE C1031 " --> pdb=" O TYR C1028 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY C1033 " --> pdb=" O MET C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1081 removed outlier: 4.402A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1083 through 1101 removed outlier: 3.940A pdb=" N GLU C1097 " --> pdb=" O ASN C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1117 removed outlier: 4.181A pdb=" N TYR C1111 " --> pdb=" O LYS C1107 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN C1112 " --> pdb=" O PHE C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1128 through 1141 Processing helix chain 'C' and resid 1163 through 1192 Processing helix chain 'C' and resid 1192 through 1231 Processing helix chain 'B' and resid 31 through 36 removed outlier: 3.748A pdb=" N PHE B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.762A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 182 removed outlier: 3.562A pdb=" N ILE B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 206 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.722A pdb=" N ASP B 229 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 334 through 343 Processing helix chain 'B' and resid 354 through 363 Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.523A pdb=" N ALA B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 420 through 431 Processing helix chain 'B' and resid 433 through 440 removed outlier: 4.014A pdb=" N ALA B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.600A pdb=" N ASP B 459 " --> pdb=" O GLN B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 493 removed outlier: 4.010A pdb=" N ASN B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 512 Processing helix chain 'B' and resid 533 through 546 removed outlier: 3.514A pdb=" N GLU B 542 " --> pdb=" O GLY B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 565 Processing helix chain 'B' and resid 614 through 625 Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.808A pdb=" N HIS B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 662 Processing helix chain 'B' and resid 666 through 694 removed outlier: 3.688A pdb=" N ASP B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.692A pdb=" N SER B 710 " --> pdb=" O LYS B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 723 through 729 Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 749 through 759 Processing helix chain 'B' and resid 835 through 845 removed outlier: 4.369A pdb=" N LYS B 840 " --> pdb=" O PRO B 836 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 845 " --> pdb=" O ILE B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 872 Processing helix chain 'B' and resid 879 through 902 Processing helix chain 'B' and resid 907 through 916 Processing helix chain 'B' and resid 918 through 939 Processing helix chain 'B' and resid 943 through 967 removed outlier: 3.635A pdb=" N ASP B 947 " --> pdb=" O PRO B 943 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 963 " --> pdb=" O TRP B 959 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 964 " --> pdb=" O TYR B 960 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP B 965 " --> pdb=" O ILE B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 1009 removed outlier: 3.892A pdb=" N TYR B 976 " --> pdb=" O TYR B 972 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1025 removed outlier: 3.853A pdb=" N LYS B1021 " --> pdb=" O TRP B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1030 removed outlier: 3.932A pdb=" N TRP B1029 " --> pdb=" O TYR B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1081 removed outlier: 4.029A pdb=" N ALA B1070 " --> pdb=" O TRP B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1120 removed outlier: 4.148A pdb=" N PHE B1096 " --> pdb=" O ASN B1092 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B1097 " --> pdb=" O ASN B1093 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE B1101 " --> pdb=" O GLU B1097 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B1103 " --> pdb=" O LYS B1099 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLN B1104 " --> pdb=" O SER B1100 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR B1111 " --> pdb=" O LYS B1107 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN B1112 " --> pdb=" O PHE B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1145 removed outlier: 3.542A pdb=" N ARG B1145 " --> pdb=" O CYS B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1190 Processing helix chain 'B' and resid 1192 through 1232 removed outlier: 3.523A pdb=" N ARG B1231 " --> pdb=" O THR B1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 removed outlier: 4.454A pdb=" N HIS A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 180 removed outlier: 3.605A pdb=" N THR A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 removed outlier: 3.584A pdb=" N SER A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.848A pdb=" N ILE A 223 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 224 " --> pdb=" O TRP A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 224' Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.607A pdb=" N ILE A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.515A pdb=" N SER A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.548A pdb=" N ILE A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 removed outlier: 3.681A pdb=" N TYR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 368 removed outlier: 3.931A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 386 removed outlier: 3.662A pdb=" N ILE A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 420 through 430 Processing helix chain 'A' and resid 433 through 439 removed outlier: 4.325A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 433 through 439' Processing helix chain 'A' and resid 453 through 462 removed outlier: 3.580A pdb=" N LEU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.612A pdb=" N LEU A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 501 through 514 removed outlier: 3.536A pdb=" N ARG A 507 " --> pdb=" O TYR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 546 Processing helix chain 'A' and resid 555 through 566 removed outlier: 3.694A pdb=" N ARG A 559 " --> pdb=" O ARG A 555 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 625 removed outlier: 3.662A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 620 " --> pdb=" O HIS A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.520A pdb=" N PHE A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 659 Processing helix chain 'A' and resid 665 through 694 removed outlier: 3.570A pdb=" N SER A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 692 " --> pdb=" O ASP A 688 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 693 " --> pdb=" O GLN A 689 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 704 removed outlier: 3.646A pdb=" N LYS A 700 " --> pdb=" O GLN A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.866A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 741 removed outlier: 3.518A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 760 removed outlier: 3.514A pdb=" N GLY A 757 " --> pdb=" O LYS A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 764 removed outlier: 3.658A pdb=" N ILE A 764 " --> pdb=" O PRO A 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 764' Processing helix chain 'A' and resid 835 through 845 removed outlier: 3.659A pdb=" N ARG A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 872 removed outlier: 3.736A pdb=" N TYR A 855 " --> pdb=" O LYS A 851 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 870 " --> pdb=" O PHE A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 902 removed outlier: 3.594A pdb=" N ILE A 889 " --> pdb=" O VAL A 885 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 891 " --> pdb=" O SER A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 917 removed outlier: 3.710A pdb=" N LYS A 913 " --> pdb=" O LEU A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 940 removed outlier: 3.822A pdb=" N VAL A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 923 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 927 " --> pdb=" O THR A 923 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 962 removed outlier: 3.520A pdb=" N TYR A 952 " --> pdb=" O GLY A 948 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS A 953 " --> pdb=" O ARG A 949 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 955 " --> pdb=" O ILE A 951 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE A 957 " --> pdb=" O CYS A 953 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR A 958 " --> pdb=" O VAL A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 966 Processing helix chain 'A' and resid 972 through 1010 removed outlier: 3.616A pdb=" N GLY A 981 " --> pdb=" O VAL A 977 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 982 " --> pdb=" O MET A 978 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1029 removed outlier: 3.675A pdb=" N LYS A1021 " --> pdb=" O TRP A1017 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET A1026 " --> pdb=" O ASN A1022 " (cutoff:3.500A) Proline residue: A1027 - end of helix Processing helix chain 'A' and resid 1036 through 1040 removed outlier: 3.725A pdb=" N ILE A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1080 removed outlier: 4.241A pdb=" N ALA A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1093 removed outlier: 3.985A pdb=" N PHE A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1120 removed outlier: 3.968A pdb=" N GLN A1104 " --> pdb=" O SER A1100 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A1113 " --> pdb=" O GLN A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1141 Processing helix chain 'A' and resid 1163 through 1190 removed outlier: 3.679A pdb=" N LYS A1169 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A1173 " --> pdb=" O LYS A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1232 removed outlier: 3.620A pdb=" N ASN A1206 " --> pdb=" O GLU A1202 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A1216 " --> pdb=" O GLU A1212 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER A1220 " --> pdb=" O GLU A1216 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A1221 " --> pdb=" O ARG A1217 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU A1225 " --> pdb=" O MET A1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 163 through 181 removed outlier: 3.705A pdb=" N LYS D 172 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 209 removed outlier: 3.697A pdb=" N SER D 207 " --> pdb=" O LYS D 203 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS D 208 " --> pdb=" O ASP D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 314 through 319 Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 339 through 345 Processing helix chain 'D' and resid 353 through 365 Processing helix chain 'D' and resid 371 through 386 removed outlier: 3.533A pdb=" N GLN D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 378 " --> pdb=" O GLN D 374 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 380 " --> pdb=" O GLN D 376 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE D 381 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 410 through 415 Processing helix chain 'D' and resid 420 through 432 removed outlier: 3.917A pdb=" N SER D 426 " --> pdb=" O PRO D 422 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 removed outlier: 4.268A pdb=" N VAL D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 476 removed outlier: 3.821A pdb=" N LYS D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 removed outlier: 3.503A pdb=" N LEU D 483 " --> pdb=" O MET D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 501 through 514 removed outlier: 3.714A pdb=" N ARG D 507 " --> pdb=" O TYR D 503 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 545 Processing helix chain 'D' and resid 555 through 566 removed outlier: 3.616A pdb=" N LEU D 561 " --> pdb=" O ARG D 557 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS D 563 " --> pdb=" O ARG D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 625 removed outlier: 4.238A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET D 625 " --> pdb=" O TRP D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.977A pdb=" N TRP D 635 " --> pdb=" O ALA D 631 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 662 removed outlier: 4.174A pdb=" N SER D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 694 removed outlier: 3.513A pdb=" N VAL D 684 " --> pdb=" O GLY D 680 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN D 689 " --> pdb=" O GLU D 685 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 692 " --> pdb=" O ASP D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 704 removed outlier: 3.832A pdb=" N LYS D 700 " --> pdb=" O GLN D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 722 removed outlier: 3.510A pdb=" N ALA D 720 " --> pdb=" O GLN D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 729 Processing helix chain 'D' and resid 729 through 742 Processing helix chain 'D' and resid 751 through 760 removed outlier: 3.562A pdb=" N LEU D 759 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 767 Processing helix chain 'D' and resid 835 through 845 Processing helix chain 'D' and resid 847 through 872 removed outlier: 3.633A pdb=" N ILE D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 902 removed outlier: 3.586A pdb=" N ILE D 884 " --> pdb=" O THR D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 917 removed outlier: 3.597A pdb=" N LYS D 913 " --> pdb=" O LEU D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 939 removed outlier: 3.521A pdb=" N LEU D 925 " --> pdb=" O ASN D 921 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 926 " --> pdb=" O VAL D 922 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA D 927 " --> pdb=" O THR D 923 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 937 " --> pdb=" O VAL D 933 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 962 removed outlier: 3.664A pdb=" N TYR D 952 " --> pdb=" O GLY D 948 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D 955 " --> pdb=" O ILE D 951 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 956 " --> pdb=" O TYR D 952 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D 957 " --> pdb=" O CYS D 953 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR D 958 " --> pdb=" O VAL D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 967 removed outlier: 3.875A pdb=" N ILE D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 970 No H-bonds generated for 'chain 'D' and resid 968 through 970' Processing helix chain 'D' and resid 972 through 1010 removed outlier: 3.574A pdb=" N GLY D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS D 982 " --> pdb=" O MET D 978 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D1004 " --> pdb=" O SER D1000 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D1008 " --> pdb=" O ALA D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1029 removed outlier: 3.692A pdb=" N LYS D1021 " --> pdb=" O TRP D1017 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET D1026 " --> pdb=" O ASN D1022 " (cutoff:3.500A) Proline residue: D1027 - end of helix Processing helix chain 'D' and resid 1036 through 1040 removed outlier: 3.854A pdb=" N ILE D1040 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1081 removed outlier: 4.102A pdb=" N ALA D1070 " --> pdb=" O TRP D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1120 removed outlier: 3.730A pdb=" N LEU D1087 " --> pdb=" O LEU D1083 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D1096 " --> pdb=" O ASN D1092 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU D1097 " --> pdb=" O ASN D1093 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D1098 " --> pdb=" O THR D1094 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE D1101 " --> pdb=" O GLU D1097 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLN D1104 " --> pdb=" O SER D1100 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D1117 " --> pdb=" O LEU D1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 1127 through 1145 removed outlier: 3.717A pdb=" N SER D1131 " --> pdb=" O LEU D1127 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET D1133 " --> pdb=" O ILE D1129 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D1143 " --> pdb=" O HIS D1139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP D1144 " --> pdb=" O LEU D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1190 removed outlier: 4.210A pdb=" N PHE D1173 " --> pdb=" O LYS D1169 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP D1186 " --> pdb=" O PHE D1182 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1228 removed outlier: 3.603A pdb=" N MET D1209 " --> pdb=" O GLU D1205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AA2, first strand: chain 'C' and resid 232 through 240 removed outlier: 6.878A pdb=" N PHE C 106 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR C 239 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU C 110 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA C 105 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C 107 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N PHE C 259 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET C 121 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N LEU C 261 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 123 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 218 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE C 151 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL C 327 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA C 301 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N CYS C 329 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 303 " --> pdb=" O CYS C 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 40 Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 240 removed outlier: 6.284A pdb=" N PHE B 106 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR B 108 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR B 239 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU B 110 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ALA B 105 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY B 107 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B 122 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL B 123 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR B 215 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE B 260 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY B 217 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA B 262 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA B 219 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ILE B 185 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 218 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 187 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE B 151 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU B 150 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 302 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N SER B 152 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL B 327 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ALA B 301 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL B 326 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 37 through 40 Processing sheet with id=AA6, first strand: chain 'A' and resid 105 through 108 removed outlier: 6.154A pdb=" N THR A 108 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 236 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 121 through 124 removed outlier: 7.440A pdb=" N MET A 121 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N LEU A 261 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A 123 " --> pdb=" O LEU A 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 184 through 186 Processing sheet with id=AA9, first strand: chain 'D' and resid 37 through 38 Processing sheet with id=AB1, first strand: chain 'D' and resid 216 through 217 removed outlier: 9.437A pdb=" N PHE D 259 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET D 121 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 120 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE D 106 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG D 237 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR D 108 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR D 239 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU D 110 " --> pdb=" O TYR D 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 125 through 126 removed outlier: 7.013A pdb=" N VAL D 125 " --> pdb=" O ASP D 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 184 through 186 1804 hydrogen bonds defined for protein. 5356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5960 1.33 - 1.45: 8527 1.45 - 1.58: 17565 1.58 - 1.71: 4 1.71 - 1.84: 368 Bond restraints: 32424 Sorted by residual: bond pdb=" C ILE B 835 " pdb=" N PRO B 836 " ideal model delta sigma weight residual 1.333 1.428 -0.094 1.44e-02 4.82e+03 4.29e+01 bond pdb=" C PRO D 761 " pdb=" N PRO D 762 " ideal model delta sigma weight residual 1.337 1.406 -0.069 1.11e-02 8.12e+03 3.87e+01 bond pdb=" C MET B1026 " pdb=" N PRO B1027 " ideal model delta sigma weight residual 1.334 1.418 -0.083 1.51e-02 4.39e+03 3.05e+01 bond pdb=" C GLU A 904 " pdb=" N PRO A 905 " ideal model delta sigma weight residual 1.332 1.403 -0.071 1.30e-02 5.92e+03 3.01e+01 bond pdb=" C ILE C 835 " pdb=" N PRO C 836 " ideal model delta sigma weight residual 1.335 1.408 -0.073 1.38e-02 5.25e+03 2.83e+01 ... (remaining 32419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 41299 2.90 - 5.79: 2413 5.79 - 8.69: 398 8.69 - 11.58: 66 11.58 - 14.48: 23 Bond angle restraints: 44199 Sorted by residual: angle pdb=" N ILE A1031 " pdb=" CA ILE A1031 " pdb=" C ILE A1031 " ideal model delta sigma weight residual 112.83 105.31 7.52 9.90e-01 1.02e+00 5.77e+01 angle pdb=" N ILE A 441 " pdb=" CA ILE A 441 " pdb=" C ILE A 441 " ideal model delta sigma weight residual 112.83 105.40 7.43 9.90e-01 1.02e+00 5.63e+01 angle pdb=" N ASP A 941 " pdb=" CA ASP A 941 " pdb=" C ASP A 941 " ideal model delta sigma weight residual 110.53 120.18 -9.65 1.29e+00 6.01e-01 5.60e+01 angle pdb=" C ILE D1067 " pdb=" N VAL D1068 " pdb=" CA VAL D1068 " ideal model delta sigma weight residual 120.24 124.78 -4.54 6.30e-01 2.52e+00 5.19e+01 angle pdb=" N LEU D 413 " pdb=" CA LEU D 413 " pdb=" C LEU D 413 " ideal model delta sigma weight residual 113.88 105.75 8.13 1.23e+00 6.61e-01 4.37e+01 ... (remaining 44194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 17870 17.99 - 35.98: 1513 35.98 - 53.97: 284 53.97 - 71.96: 55 71.96 - 89.95: 21 Dihedral angle restraints: 19743 sinusoidal: 7674 harmonic: 12069 Sorted by residual: dihedral pdb=" CB CYS C1044 " pdb=" SG CYS C1044 " pdb=" SG CYS C1061 " pdb=" CB CYS C1061 " ideal model delta sinusoidal sigma weight residual -86.00 0.85 -86.85 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS B1044 " pdb=" SG CYS B1044 " pdb=" SG CYS B1061 " pdb=" CB CYS B1061 " ideal model delta sinusoidal sigma weight residual -86.00 -165.25 79.25 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS D1044 " pdb=" SG CYS D1044 " pdb=" SG CYS D1061 " pdb=" CB CYS D1061 " ideal model delta sinusoidal sigma weight residual 93.00 16.10 76.90 1 1.00e+01 1.00e-02 7.42e+01 ... (remaining 19740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 4847 0.155 - 0.310: 270 0.310 - 0.465: 22 0.465 - 0.620: 3 0.620 - 0.775: 2 Chirality restraints: 5144 Sorted by residual: chirality pdb=" CB ILE D 109 " pdb=" CA ILE D 109 " pdb=" CG1 ILE D 109 " pdb=" CG2 ILE D 109 " both_signs ideal model delta sigma weight residual False 2.64 1.87 0.78 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" CG LEU C 687 " pdb=" CB LEU C 687 " pdb=" CD1 LEU C 687 " pdb=" CD2 LEU C 687 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CB THR C 484 " pdb=" CA THR C 484 " pdb=" OG1 THR C 484 " pdb=" CG2 THR C 484 " both_signs ideal model delta sigma weight residual False 2.55 2.00 0.55 2.00e-01 2.50e+01 7.50e+00 ... (remaining 5141 not shown) Planarity restraints: 5516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " 0.063 2.00e-02 2.50e+03 6.01e-02 9.03e+01 pdb=" CG TRP B 142 " -0.156 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " 0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 431 " 0.027 2.00e-02 2.50e+03 3.69e-02 3.40e+01 pdb=" CG TRP B 431 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP B 431 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TRP B 431 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 431 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B 431 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 431 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 431 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 431 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 431 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1001 " -0.046 2.00e-02 2.50e+03 4.32e-02 3.27e+01 pdb=" CG PHE A1001 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 PHE A1001 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE A1001 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A1001 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A1001 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE A1001 " -0.003 2.00e-02 2.50e+03 ... (remaining 5513 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 7529 2.80 - 3.32: 32584 3.32 - 3.85: 53070 3.85 - 4.37: 62291 4.37 - 4.90: 98896 Nonbonded interactions: 254370 Sorted by model distance: nonbonded pdb=" O ILE A1129 " pdb=" N HIS A1132 " model vdw 2.274 3.120 nonbonded pdb=" O LEU A1127 " pdb=" N ILE A1129 " model vdw 2.339 3.120 nonbonded pdb=" O PRO D 943 " pdb=" OG SER D 946 " model vdw 2.355 3.040 nonbonded pdb=" O ILE A1129 " pdb=" N SER A1131 " model vdw 2.374 3.120 nonbonded pdb=" O LEU B 471 " pdb=" N GLU B 474 " model vdw 2.390 3.120 ... (remaining 254365 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 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 43 or (resid 44 through 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 through 137 or (resid 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 o \ r (resid 141 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 42 through 183 or (resid 184 and (name N or name CA or name C or name O or name \ CB )) or resid 185 through 207 or resid 213 through 222 or (resid 223 and (name \ N or name CA or name C or name O or name CB )) or resid 224 through 229 or (resi \ d 230 and (name N or name CA or name C or name O or name CB )) or resid 231 thro \ ugh 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) o \ r resid 261 through 273 or (resid 274 through 275 and (name N or name CA or name \ C or name O or name CB )) or resid 276 through 279 or (resid 280 through 282 an \ d (name N or name CA or name C or name O or name CB )) or resid 283 through 301 \ or (resid 302 and (name N or name CA or name C or name O or name CB )) or resid \ 303 through 312 or (resid 313 and (name N or name CA or name C or name O or name \ CB )) or resid 314 through 317 or (resid 318 through 319 and (name N or name CA \ or name C or name O or name CB )) or resid 320 through 342 or (resid 343 and (n \ ame N or name CA or name C or name O or name CB )) or resid 344 through 369 or ( \ resid 370 and (name N or name CA or name C or name O or name CB )) or resid 371 \ through 385 or (resid 386 through 387 and (name N or name CA or name C or name O \ or name CB )) or resid 388 through 390 or (resid 391 through 392 and (name N or \ name CA or name C or name O or name CB )) or resid 393 through 398 or (resid 40 \ 3 through 404 and (name N or name CA or name C or name O or name CB )) or resid \ 405 or (resid 406 and (name N or name CA or name C or name O or name CB )) or re \ sid 407 through 409 or (resid 410 and (name N or name CA or name C or name O or \ name CB )) or resid 411 through 412 or (resid 413 through 415 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 416 through 421 and (name N or \ name CA or name C or name O or name CB )) or resid 422 through 424 or (resid 425 \ and (name N or name CA or name C or name O or name CB )) or resid 426 through 4 \ 28 or (resid 429 through 430 and (name N or name CA or name C or name O or name \ CB )) or resid 431 through 432 or (resid 433 through 435 and (name N or name CA \ or name C or name O or name CB )) or resid 436 through 441 or (resid 442 through \ 444 and (name N or name CA or name C or name O or name CB )) or resid 445 throu \ gh 451 or (resid 452 and (name N or name CA or name C or name O or name CB )) or \ resid 453 through 457 or (resid 458 and (name N or name CA or name C or name O \ or name CB )) or resid 459 through 461 or (resid 462 and (name N or name CA or n \ ame C or name O or name CB )) or resid 463 or (resid 464 through 466 and (name N \ or name CA or name C or name O or name CB )) or resid 467 or (resid 468 and (na \ me N or name CA or name C or name O or name CB )) or resid 469 through 482 or (r \ esid 483 and (name N or name CA or name C or name O or name CB )) or resid 484 t \ hrough 486 or (resid 487 through 490 and (name N or name CA or name C or name O \ or name CB )) or resid 491 through 498 or (resid 499 through 500 and (name N or \ name CA or name C or name O or name CB )) or resid 501 through 504 or (resid 505 \ and (name N or name CA or name C or name O or name CB )) or resid 506 through 5 \ 09 or (resid 510 through 514 and (name N or name CA or name C or name O or name \ CB )) or resid 528 or (resid 529 through 531 and (name N or name CA or name C or \ name O or name CB )) or resid 532 through 536 or (resid 537 and (name N or name \ CA or name C or name O or name CB )) or resid 538 or (resid 539 and (name N or \ name CA or name C or name O or name CB )) or resid 540 through 544 or (resid 545 \ and (name N or name CA or name C or name O or name CB )) or resid 546 through 5 \ 54 or (resid 555 through 557 and (name N or name CA or name C or name O or name \ CB )) or resid 558 through 618 or (resid 619 and (name N or name CA or name C or \ name O or name CB )) or resid 620 through 654 or (resid 655 through 656 and (na \ me N or name CA or name C or name O or name CB )) or resid 657 through 661 or (r \ esid 662 and (name N or name CA or name C or name O or name CB )) or resid 663 t \ hrough 670 or (resid 671 and (name N or name CA or name C or name O or name CB ) \ ) or resid 672 through 673 or resid 675 through 676 or (resid 677 and (name N or \ name CA or name C or name O or name CB )) or resid 678 through 742 or (resid 74 \ 3 through 748 and (name N or name CA or name C or name O or name CB )) or resid \ 749 through 934 or (resid 935 and (name N or name CA or name C or name O or name \ CB )) or resid 936 through 944 or (resid 945 and (name N or name CA or name C o \ r name O or name CB )) or resid 946 through 955 or (resid 956 and (name N or nam \ e CA or name C or name O or name CB )) or resid 957 through 1045 or resid 1058 t \ hrough 1061 or (resid 1062 and (name N or name CA or name C or name O or name CB \ )) or resid 1063 through 1129 or (resid 1130 and (name N or name CA or name C o \ r name O or name CB )) or resid 1131 through 1132 or (resid 1133 and (name N or \ name CA or name C or name O or name CB )) or resid 1134 through 1138 or (resid 1 \ 139 and (name N or name CA or name C or name O or name CB )) or resid 1140 throu \ gh 1164 or (resid 1165 and (name N or name CA or name C or name O or name CB )) \ or resid 1166 through 1168 or (resid 1169 and (name N or name CA or name C or na \ me O or name CB )) or resid 1170 through 1187 or (resid 1188 and (name N or name \ CA or name C or name O or name CB )) or resid 1189 through 1201 or (resid 1202 \ and (name N or name CA or name C or name O or name CB )) or resid 1203 through 1 \ 208 or (resid 1209 through 1210 and (name N or name CA or name C or name O or na \ me CB )) or resid 1211 through 1403)) selection = (chain 'B' and (resid 30 through 43 or (resid 44 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 145 or (resid 146 and ( \ name N or name CA or name C or name O or name CB )) or resid 147 through 203 or \ (resid 204 and (name N or name CA or name C or name O or name CB )) or resid 205 \ through 254 or (resid 255 and (name N or name CA or name C or name O or name CB \ )) or resid 256 through 273 or (resid 274 through 275 and (name N or name CA or \ name C or name O or name CB )) or resid 276 through 279 or (resid 280 through 2 \ 82 and (name N or name CA or name C or name O or name CB )) or resid 283 through \ 285 or (resid 286 and (name N or name CA or name C or name O or name CB )) or r \ esid 287 through 312 or (resid 313 and (name N or name CA or name C or name O or \ name CB )) or resid 314 through 398 or (resid 403 through 404 and (name N or na \ me CA or name C or name O or name CB )) or resid 405 through 412 or (resid 413 t \ hrough 415 and (name N or name CA or name C or name O or name CB )) or resid 416 \ through 424 or (resid 425 and (name N or name CA or name C or name O or name CB \ )) or resid 426 through 432 or (resid 433 through 435 and (name N or name CA or \ name C or name O or name CB )) or resid 436 through 437 or (resid 438 and (name \ N or name CA or name C or name O or name CB )) or resid 439 through 441 or (res \ id 442 through 444 and (name N or name CA or name C or name O or name CB )) or r \ esid 445 through 446 or (resid 447 and (name N or name CA or name C or name O or \ name CB )) or resid 448 through 461 or (resid 462 and (name N or name CA or nam \ e C or name O or name CB )) or resid 463 or (resid 464 through 466 and (name N o \ r name CA or name C or name O or name CB )) or resid 467 or (resid 468 and (name \ N or name CA or name C or name O or name CB )) or resid 469 through 473 or (res \ id 474 and (name N or name CA or name C or name O or name CB )) or resid 475 thr \ ough 480 or (resid 481 and (name N or name CA or name C or name O or name CB )) \ or resid 482 through 486 or (resid 487 through 490 and (name N or name CA or nam \ e C or name O or name CB )) or resid 491 through 494 or (resid 495 and (name N o \ r name CA or name C or name O or name CB )) or resid 496 through 499 or (resid 5 \ 00 and (name N or name CA or name C or name O or name CB )) or resid 501 through \ 511 or (resid 512 through 514 and (name N or name CA or name C or name O or nam \ e CB )) or resid 528 or (resid 529 through 531 and (name N or name CA or name C \ or name O or name CB )) or resid 532 through 535 or (resid 536 through 537 and ( \ name N or name CA or name C or name O or name CB )) or resid 538 or (resid 539 a \ nd (name N or name CA or name C or name O or name CB )) or resid 540 through 544 \ or (resid 545 and (name N or name CA or name C or name O or name CB )) or resid \ 546 through 554 or (resid 555 through 557 and (name N or name CA or name C or n \ ame O or name CB )) or resid 558 through 562 or (resid 563 through 608 and (name \ N or name CA or name C or name O or name CB )) or resid 609 through 623 or (res \ id 624 and (name N or name CA or name C or name O or name CB )) or resid 625 thr \ ough 628 or (resid 629 and (name N or name CA or name C or name O or name CB )) \ or resid 630 through 652 or (resid 653 through 656 and (name N or name CA or nam \ e C or name O or name CB )) or resid 657 through 660 or (resid 661 through 662 a \ nd (name N or name CA or name C or name O or name CB )) or resid 663 through 665 \ or (resid 666 through 667 and (name N or name CA or name C or name O or name CB \ )) or resid 668 through 670 or (resid 671 and (name N or name CA or name C or n \ ame O or name CB )) or resid 672 through 673 or resid 675 through 704 or (resid \ 705 and (name N or name CA or name C or name O or name CB )) or resid 706 throug \ h 742 or (resid 743 through 748 and (name N or name CA or name C or name O or na \ me CB )) or resid 749 through 767 or (resid 768 and (name N or name CA or name C \ or name O or name CB )) or resid 769 or (resid 834 through 835 and (name N or n \ ame CA or name C or name O or name CB )) or resid 836 or (resid 837 and (name N \ or name CA or name C or name O or name CB )) or resid 838 or (resid 839 and (nam \ e N or name CA or name C or name O or name CB )) or resid 840 through 842 or (re \ sid 843 and (name N or name CA or name C or name O or name CB )) or resid 844 th \ rough 903 or (resid 904 and (name N or name CA or name C or name O or name CB )) \ or resid 905 through 917 or (resid 918 and (name N or name CA or name C or name \ O or name CB )) or resid 919 through 944 or (resid 945 and (name N or name CA o \ r name C or name O or name CB )) or resid 946 through 986 or (resid 987 and (nam \ e N or name CA or name C or name O or name CB )) or resid 988 through 1017 or (r \ esid 1018 and (name N or name CA or name C or name O or name CB )) or resid 1019 \ through 1045 or resid 1058 through 1098 or (resid 1099 and (name N or name CA o \ r name C or name O or name CB )) or resid 1100 through 1111 or (resid 1112 and ( \ name N or name CA or name C or name O or name CB )) or resid 1113 through 1118 o \ r (resid 1119 and (name N or name CA or name C or name O or name CB )) or resid \ 1120 through 1129 or (resid 1130 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1131 through 1134 or (resid 1135 and (name N or name CA or na \ me C or name O or name CB )) or resid 1136 through 1142 or resid 1159 through 11 \ 60 or (resid 1161 and (name N or name CA or name C or name O or name CB )) or re \ sid 1162 through 1164 or (resid 1165 and (name N or name CA or name C or name O \ or name CB )) or resid 1166 through 1168 or (resid 1169 and (name N or name CA o \ r name C or name O or name CB )) or resid 1170 through 1187 or (resid 1188 and ( \ name N or name CA or name C or name O or name CB )) or resid 1189 through 1194 o \ r (resid 1195 and (name N or name CA or name C or name O or name CB )) or resid \ 1196 through 1211 or (resid 1212 through 1213 and (name N or name CA or name C o \ r name O or name CB )) or resid 1214 through 1217 or (resid 1218 through 1232 an \ d (name N or name CA or name C or name O or name CB )) or resid 1401 through 140 \ 3)) selection = (chain 'C' and (resid 30 through 44 or (resid 45 and (name N or name CA or name \ C or name O or name CB )) or resid 46 through 140 or (resid 141 and (name N or n \ ame CA or name C or name O or name CB )) or resid 142 through 145 or (resid 146 \ and (name N or name CA or name C or name O or name CB )) or resid 147 through 18 \ 3 or (resid 184 and (name N or name CA or name C or name O or name CB )) or resi \ d 185 through 203 or (resid 204 and (name N or name CA or name C or name O or na \ me CB )) or resid 205 through 222 or (resid 223 and (name N or name CA or name C \ or name O or name CB )) or resid 224 through 254 or (resid 255 and (name N or n \ ame CA or name C or name O or name CB )) or resid 256 through 273 or (resid 274 \ through 275 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 6 through 279 or (resid 280 through 282 and (name N or name CA or name C or name \ O or name CB )) or resid 283 through 285 or (resid 286 and (name N or name CA o \ r name C or name O or name CB )) or resid 287 through 301 or (resid 302 and (nam \ e N or name CA or name C or name O or name CB )) or resid 303 through 312 or (re \ sid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 th \ rough 317 or (resid 318 through 319 and (name N or name CA or name C or name O o \ r name CB )) or resid 320 through 390 or (resid 391 through 392 and (name N or n \ ame CA or name C or name O or name CB )) or resid 393 through 405 or (resid 406 \ and (name N or name CA or name C or name O or name CB )) or resid 407 through 40 \ 9 or (resid 410 and (name N or name CA or name C or name O or name CB )) or resi \ d 411 through 412 or (resid 413 through 415 and (name N or name CA or name C or \ name O or name CB )) or resid 416 through 424 or (resid 425 and (name N or name \ CA or name C or name O or name CB )) or resid 426 through 432 or (resid 433 thro \ ugh 435 and (name N or name CA or name C or name O or name CB )) or resid 436 th \ rough 437 or (resid 438 and (name N or name CA or name C or name O or name CB )) \ or resid 439 through 441 or (resid 442 through 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 446 or (resid 447 and (name N \ or name CA or name C or name O or name CB )) or resid 448 through 457 or (resid \ 458 and (name N or name CA or name C or name O or name CB )) or resid 459 throug \ h 461 or (resid 462 and (name N or name CA or name C or name O or name CB )) or \ resid 463 or (resid 464 through 466 and (name N or name CA or name C or name O o \ r name CB )) or resid 467 or (resid 468 and (name N or name CA or name C or name \ O or name CB )) or resid 469 through 473 or (resid 474 and (name N or name CA o \ r name C or name O or name CB )) or resid 475 through 480 or (resid 481 and (nam \ e N or name CA or name C or name O or name CB )) or resid 482 or (resid 483 and \ (name N or name CA or name C or name O or name CB )) or resid 484 through 486 or \ (resid 487 through 490 and (name N or name CA or name C or name O or name CB )) \ or resid 491 through 494 or (resid 495 and (name N or name CA or name C or name \ O or name CB )) or resid 496 through 499 or (resid 500 and (name N or name CA o \ r name C or name O or name CB )) or resid 501 through 511 or (resid 512 through \ 514 and (name N or name CA or name C or name O or name CB )) or resid 528 or (re \ sid 529 through 531 and (name N or name CA or name C or name O or name CB )) or \ resid 532 through 535 or (resid 536 through 537 and (name N or name CA or name C \ or name O or name CB )) or resid 538 or (resid 539 and (name N or name CA or na \ me C or name O or name CB )) or resid 540 through 544 or (resid 545 and (name N \ or name CA or name C or name O or name CB )) or resid 546 through 562 or (resid \ 563 through 608 and (name N or name CA or name C or name O or name CB )) or resi \ d 609 through 618 or (resid 619 and (name N or name CA or name C or name O or na \ me CB )) or resid 620 through 628 or (resid 629 and (name N or name CA or name C \ or name O or name CB )) or resid 630 through 652 or (resid 653 through 656 and \ (name N or name CA or name C or name O or name CB )) or resid 657 through 660 or \ (resid 661 through 662 and (name N or name CA or name C or name O or name CB )) \ or resid 663 or (resid 664 through 667 and (name N or name CA or name C or name \ O or name CB )) or resid 668 through 673 or resid 675 through 676 or (resid 677 \ and (name N or name CA or name C or name O or name CB )) or resid 678 through 7 \ 04 or (resid 705 and (name N or name CA or name C or name O or name CB )) or res \ id 706 through 759 or (resid 760 and (name N or name CA or name C or name O or n \ ame CB )) or resid 761 through 767 or (resid 768 and (name N or name CA or name \ C or name O or name CB )) or resid 769 or (resid 834 through 835 and (name N or \ name CA or name C or name O or name CB )) or resid 836 or (resid 837 and (name N \ or name CA or name C or name O or name CB )) or resid 838 or (resid 839 and (na \ me N or name CA or name C or name O or name CB )) or resid 840 through 842 or (r \ esid 843 and (name N or name CA or name C or name O or name CB )) or resid 844 t \ hrough 903 or (resid 904 and (name N or name CA or name C or name O or name CB ) \ ) or resid 905 through 917 or (resid 918 and (name N or name CA or name C or nam \ e O or name CB )) or resid 919 through 944 or (resid 945 and (name N or name CA \ or name C or name O or name CB )) or resid 946 through 986 or (resid 987 and (na \ me N or name CA or name C or name O or name CB )) or resid 988 through 1017 or ( \ resid 1018 and (name N or name CA or name C or name O or name CB )) or resid 101 \ 9 through 1045 or resid 1058 through 1098 or (resid 1099 and (name N or name CA \ or name C or name O or name CB )) or resid 1100 through 1111 or (resid 1112 and \ (name N or name CA or name C or name O or name CB )) or resid 1113 through 1118 \ or (resid 1119 and (name N or name CA or name C or name O or name CB )) or resid \ 1120 through 1129 or (resid 1130 and (name N or name CA or name C or name O or \ name CB )) or resid 1131 through 1134 or (resid 1135 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1136 through 1142 or (resid 1159 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1160 or (resid 1161 an \ d (name N or name CA or name C or name O or name CB )) or resid 1162 through 116 \ 4 or (resid 1165 and (name N or name CA or name C or name O or name CB )) or res \ id 1166 through 1167 or (resid 1168 through 1169 and (name N or name CA or name \ C or name O or name CB )) or resid 1170 through 1187 or (resid 1188 and (name N \ or name CA or name C or name O or name CB )) or resid 1189 through 1194 or (resi \ d 1195 and (name N or name CA or name C or name O or name CB )) or resid 1196 th \ rough 1208 or (resid 1209 through 1210 and (name N or name CA or name C or name \ O or name CB )) or resid 1211 or (resid 1212 through 1213 and (name N or name CA \ or name C or name O or name CB )) or resid 1214 through 1219 or (resid 1220 thr \ ough 1232 and (name N or name CA or name C or name O or name CB )) or resid 1401 \ through 1403)) selection = (chain 'D' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 43 or (resid 44 through 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 through 137 or (resid 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 o \ r (resid 141 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 42 through 145 or (resid 146 and (name N or name CA or name C or name O or name \ CB )) or resid 147 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB )) or resid 185 through 207 or resid 213 through 259 or (resi \ d 260 and (name N or name CA or name C or name O or name CB )) or resid 261 thro \ ugh 301 or (resid 302 and (name N or name CA or name C or name O or name CB )) o \ r resid 303 through 317 or (resid 318 through 319 and (name N or name CA or name \ C or name O or name CB )) or resid 320 through 342 or (resid 343 and (name N or \ name CA or name C or name O or name CB )) or resid 344 through 369 or (resid 37 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 371 through \ 385 or (resid 386 through 387 and (name N or name CA or name C or name O or name \ CB )) or resid 388 through 390 or (resid 391 through 392 and (name N or name CA \ or name C or name O or name CB )) or resid 393 through 398 or (resid 403 throug \ h 404 and (name N or name CA or name C or name O or name CB )) or resid 405 or ( \ resid 406 and (name N or name CA or name C or name O or name CB )) or resid 407 \ through 409 or (resid 410 and (name N or name CA or name C or name O or name CB \ )) or resid 411 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 421 and (name N or name CA \ or name C or name O or name CB )) or resid 422 through 428 or (resid 429 through \ 430 and (name N or name CA or name C or name O or name CB )) or resid 431 throu \ gh 433 or (resid 434 through 435 and (name N or name CA or name C or name O or n \ ame CB )) or resid 436 through 437 or (resid 438 and (name N or name CA or name \ C or name O or name CB )) or resid 439 through 451 or (resid 452 and (name N or \ name CA or name C or name O or name CB )) or resid 453 through 457 or (resid 458 \ and (name N or name CA or name C or name O or name CB )) or resid 459 through 4 \ 82 or (resid 483 and (name N or name CA or name C or name O or name CB )) or res \ id 484 through 488 or (resid 489 through 490 and (name N or name CA or name C or \ name O or name CB )) or resid 491 through 498 or (resid 499 through 500 and (na \ me N or name CA or name C or name O or name CB )) or resid 501 through 509 or (r \ esid 510 through 514 and (name N or name CA or name C or name O or name CB )) or \ resid 528 through 556 or (resid 557 and (name N or name CA or name C or name O \ or name CB )) or resid 558 through 618 or (resid 619 and (name N or name CA or n \ ame C or name O or name CB )) or resid 620 through 623 or (resid 624 and (name N \ or name CA or name C or name O or name CB )) or resid 625 through 652 or (resid \ 653 through 656 and (name N or name CA or name C or name O or name CB )) or res \ id 657 through 661 or (resid 662 and (name N or name CA or name C or name O or n \ ame CB )) or resid 663 through 670 or (resid 671 and (name N or name CA or name \ C or name O or name CB )) or resid 672 through 673 or resid 675 through 676 or ( \ resid 677 and (name N or name CA or name C or name O or name CB )) or resid 678 \ through 704 or (resid 705 and (name N or name CA or name C or name O or name CB \ )) or resid 706 through 743 or (resid 744 through 748 and (name N or name CA or \ name C or name O or name CB )) or resid 749 through 769 or resid 834 through 934 \ or (resid 935 and (name N or name CA or name C or name O or name CB )) or resid \ 936 through 955 or (resid 956 and (name N or name CA or name C or name O or nam \ e CB )) or resid 957 through 1061 or (resid 1062 and (name N or name CA or name \ C or name O or name CB )) or resid 1063 through 1098 or (resid 1099 and (name N \ or name CA or name C or name O or name CB )) or resid 1100 through 1132 or (resi \ d 1133 and (name N or name CA or name C or name O or name CB )) or resid 1134 or \ (resid 1135 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 136 through 1138 or (resid 1139 and (name N or name CA or name C or name O or na \ me CB )) or resid 1140 through 1142 or (resid 1159 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1160 or (resid 1161 and (name N or name CA \ or name C or name O or name CB )) or resid 1162 through 1201 or (resid 1202 and \ (name N or name CA or name C or name O or name CB )) or resid 1203 through 1208 \ or (resid 1209 through 1210 and (name N or name CA or name C or name O or name C \ B )) or resid 1211 through 1403)) } 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.070 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.070 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.009 0.139 32428 Z= 0.481 Angle : 1.554 14.480 44207 Z= 0.899 Chirality : 0.082 0.775 5144 Planarity : 0.012 0.121 5516 Dihedral : 14.052 89.949 11915 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.23 % Favored : 92.69 % Rotamer: Outliers : 1.23 % Allowed : 1.55 % Favored : 97.21 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.10), residues: 4081 helix: -2.64 (0.08), residues: 2482 sheet: -2.62 (0.34), residues: 190 loop : -2.87 (0.14), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.003 ARG A 550 TYR 0.069 0.006 TYR B 868 PHE 0.096 0.006 PHE A1001 TRP 0.156 0.007 TRP B 142 HIS 0.025 0.004 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00917 (32424) covalent geometry : angle 1.55390 (44199) SS BOND : bond 0.00850 ( 4) SS BOND : angle 2.39533 ( 8) hydrogen bonds : bond 0.20377 ( 1804) hydrogen bonds : angle 9.13146 ( 5356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 616 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 HIS cc_start: 0.9257 (t-90) cc_final: 0.9005 (t70) REVERT: C 242 MET cc_start: 0.2355 (tpt) cc_final: 0.2019 (tpt) REVERT: C 330 ASP cc_start: 0.8346 (t0) cc_final: 0.8127 (m-30) REVERT: C 397 MET cc_start: 0.8887 (tpp) cc_final: 0.8249 (tpt) REVERT: C 435 ASP cc_start: 0.8924 (m-30) cc_final: 0.8621 (m-30) REVERT: C 438 ARG cc_start: 0.8802 (ptp-110) cc_final: 0.8454 (ptp-110) REVERT: C 444 TYR cc_start: 0.8214 (m-80) cc_final: 0.7973 (m-80) REVERT: C 483 LEU cc_start: 0.8990 (tp) cc_final: 0.8707 (tp) REVERT: C 915 TRP cc_start: 0.8820 (t60) cc_final: 0.8476 (t60) REVERT: C 983 MET cc_start: 0.8958 (mmp) cc_final: 0.8306 (mmp) REVERT: C 1184 GLU cc_start: 0.8789 (tp30) cc_final: 0.8554 (tp30) REVERT: B 242 MET cc_start: 0.2457 (tpt) cc_final: 0.2249 (tpt) REVERT: B 545 MET cc_start: 0.8287 (tpp) cc_final: 0.7893 (tpp) REVERT: B 639 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7700 (tp30) REVERT: B 655 MET cc_start: 0.8698 (mtt) cc_final: 0.8460 (mtm) REVERT: B 687 LEU cc_start: 0.9593 (tp) cc_final: 0.9304 (tp) REVERT: B 741 MET cc_start: 0.9164 (mmm) cc_final: 0.8812 (mtp) REVERT: B 916 LEU cc_start: 0.9335 (mm) cc_final: 0.9018 (tt) REVERT: B 1128 ILE cc_start: 0.9413 (tp) cc_final: 0.9081 (tt) REVERT: B 1135 MET cc_start: 0.8291 (tmm) cc_final: 0.8003 (tmm) REVERT: B 1166 GLU cc_start: 0.9171 (mp0) cc_final: 0.8917 (mp0) REVERT: B 1179 GLU cc_start: 0.8706 (tp30) cc_final: 0.8481 (tp30) REVERT: A 386 MET cc_start: 0.6491 (tpp) cc_final: 0.6002 (tpp) REVERT: A 397 MET cc_start: 0.8137 (mtp) cc_final: 0.7359 (mtp) REVERT: A 404 ASP cc_start: 0.7831 (t0) cc_final: 0.7573 (t0) REVERT: A 492 TYR cc_start: 0.8644 (m-80) cc_final: 0.8441 (m-80) REVERT: A 625 MET cc_start: 0.8756 (mmt) cc_final: 0.8113 (mpp) REVERT: A 692 LYS cc_start: 0.8981 (mppt) cc_final: 0.8746 (mmtt) REVERT: A 857 LEU cc_start: 0.9164 (mm) cc_final: 0.8903 (pp) REVERT: A 1039 GLN cc_start: 0.8702 (mp10) cc_final: 0.8423 (mp10) REVERT: A 1179 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8588 (mp0) REVERT: A 1206 ASN cc_start: 0.9190 (m-40) cc_final: 0.8841 (m-40) REVERT: D 121 MET cc_start: 0.8511 (tpp) cc_final: 0.8189 (tpp) REVERT: D 457 MET cc_start: 0.9341 (mmm) cc_final: 0.8958 (mmm) REVERT: D 459 ASP cc_start: 0.8715 (m-30) cc_final: 0.8504 (m-30) REVERT: D 467 ASP cc_start: 0.8585 (p0) cc_final: 0.8317 (p0) REVERT: D 979 MET cc_start: 0.8473 (mpp) cc_final: 0.7923 (mmt) REVERT: D 1026 MET cc_start: 0.8718 (mmm) cc_final: 0.7610 (mpp) outliers start: 38 outliers final: 9 residues processed: 638 average time/residue: 0.1765 time to fit residues: 187.0884 Evaluate side-chains 456 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 447 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 994 MET Chi-restraints excluded: chain C residue 1104 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain D residue 946 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 40.0000 chunk 401 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 HIS C1104 GLN B 403 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 HIS B1080 ASN B1193 ASN A 43 HIS A 343 HIS ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 867 ASN D 921 ASN D1139 HIS D1215 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.082762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.062398 restraints weight = 231303.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.064940 restraints weight = 99100.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066565 restraints weight = 57240.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.067644 restraints weight = 39614.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.068270 restraints weight = 30896.114| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32428 Z= 0.175 Angle : 0.753 10.700 44207 Z= 0.394 Chirality : 0.044 0.293 5144 Planarity : 0.006 0.085 5516 Dihedral : 7.473 59.729 5276 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.37 % Rotamer: Outliers : 1.88 % Allowed : 9.72 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.12), residues: 4081 helix: -0.88 (0.09), residues: 2540 sheet: -2.25 (0.32), residues: 226 loop : -2.45 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1210 TYR 0.027 0.002 TYR A 345 PHE 0.032 0.002 PHE D1001 TRP 0.041 0.002 TRP B 142 HIS 0.017 0.002 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00363 (32424) covalent geometry : angle 0.75254 (44199) SS BOND : bond 0.00303 ( 4) SS BOND : angle 1.26322 ( 8) hydrogen bonds : bond 0.05769 ( 1804) hydrogen bonds : angle 5.61515 ( 5356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 496 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 444 TYR cc_start: 0.8379 (m-80) cc_final: 0.8047 (m-80) REVERT: C 558 PHE cc_start: 0.8615 (t80) cc_final: 0.8363 (t80) REVERT: C 681 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8017 (tp-100) REVERT: C 962 ARG cc_start: 0.8649 (mmm-85) cc_final: 0.8316 (tpp80) REVERT: C 987 MET cc_start: 0.8718 (tpp) cc_final: 0.8501 (tpp) REVERT: C 1187 ASP cc_start: 0.8468 (p0) cc_final: 0.8206 (p0) REVERT: C 1207 MET cc_start: 0.8924 (mmp) cc_final: 0.8394 (mmt) REVERT: B 467 ASP cc_start: 0.8079 (p0) cc_final: 0.7621 (p0) REVERT: B 655 MET cc_start: 0.8489 (mtt) cc_final: 0.8286 (mtm) REVERT: B 687 LEU cc_start: 0.9584 (tp) cc_final: 0.9282 (tp) REVERT: B 723 HIS cc_start: 0.8164 (t-90) cc_final: 0.7890 (t-90) REVERT: B 741 MET cc_start: 0.9067 (mmm) cc_final: 0.8677 (mtp) REVERT: B 916 LEU cc_start: 0.9395 (mm) cc_final: 0.8950 (tt) REVERT: B 1124 PRO cc_start: 0.8452 (Cg_exo) cc_final: 0.8242 (Cg_endo) REVERT: B 1179 GLU cc_start: 0.8659 (tp30) cc_final: 0.8165 (tp30) REVERT: A 138 MET cc_start: 0.7536 (ppp) cc_final: 0.7222 (ppp) REVERT: A 242 MET cc_start: 0.7879 (tmm) cc_final: 0.7632 (tmm) REVERT: A 386 MET cc_start: 0.6184 (tpp) cc_final: 0.5708 (tpp) REVERT: A 404 ASP cc_start: 0.7938 (t0) cc_final: 0.7686 (t0) REVERT: A 407 LEU cc_start: 0.9365 (mm) cc_final: 0.8928 (tp) REVERT: A 558 PHE cc_start: 0.8654 (t80) cc_final: 0.8431 (t80) REVERT: A 902 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7413 (mtt) REVERT: A 935 MET cc_start: 0.8522 (tpt) cc_final: 0.8267 (tpt) REVERT: A 983 MET cc_start: 0.8879 (mmm) cc_final: 0.8587 (mmm) REVERT: A 1026 MET cc_start: 0.8772 (tpp) cc_final: 0.8149 (mmt) REVERT: A 1178 ILE cc_start: 0.9582 (mm) cc_final: 0.9285 (mt) REVERT: A 1179 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8637 (mp0) REVERT: A 1206 ASN cc_start: 0.8983 (m-40) cc_final: 0.8752 (m-40) REVERT: D 467 ASP cc_start: 0.8461 (p0) cc_final: 0.8225 (p0) REVERT: D 479 MET cc_start: 0.8051 (pmm) cc_final: 0.7799 (pmm) REVERT: D 1207 MET cc_start: 0.8643 (mmp) cc_final: 0.8336 (mmm) outliers start: 58 outliers final: 32 residues processed: 526 average time/residue: 0.1702 time to fit residues: 150.8438 Evaluate side-chains 454 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 421 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1080 ASN Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 946 SER Chi-restraints excluded: chain D residue 961 ILE Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 1101 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 311 optimal weight: 0.0170 chunk 260 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 360 optimal weight: 0.8980 chunk 3 optimal weight: 30.0000 chunk 268 optimal weight: 0.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN A 240 GLN A 675 ASN D 226 ASN D 283 HIS D 921 ASN D1080 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.081981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.062711 restraints weight = 164466.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.064863 restraints weight = 80024.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.066259 restraints weight = 49628.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067157 restraints weight = 36040.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.067783 restraints weight = 29145.765| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32428 Z= 0.153 Angle : 0.688 10.018 44207 Z= 0.353 Chirality : 0.042 0.233 5144 Planarity : 0.005 0.075 5516 Dihedral : 6.875 59.851 5265 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.71 % Favored : 95.17 % Rotamer: Outliers : 2.30 % Allowed : 12.41 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 4081 helix: -0.04 (0.10), residues: 2550 sheet: -1.98 (0.34), residues: 222 loop : -2.14 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1217 TYR 0.026 0.002 TYR A 345 PHE 0.035 0.002 PHE A1001 TRP 0.030 0.002 TRP C 621 HIS 0.008 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00332 (32424) covalent geometry : angle 0.68777 (44199) SS BOND : bond 0.00186 ( 4) SS BOND : angle 0.92771 ( 8) hydrogen bonds : bond 0.05010 ( 1804) hydrogen bonds : angle 5.07232 ( 5356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 462 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 397 MET cc_start: 0.8549 (tpt) cc_final: 0.8203 (tpt) REVERT: C 444 TYR cc_start: 0.8386 (m-80) cc_final: 0.8032 (m-80) REVERT: C 558 PHE cc_start: 0.8608 (t80) cc_final: 0.8354 (t80) REVERT: C 699 MET cc_start: 0.8387 (mmt) cc_final: 0.8024 (mmt) REVERT: C 734 MET cc_start: 0.8449 (ppp) cc_final: 0.8072 (ppp) REVERT: C 962 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8348 (tpp80) REVERT: C 1072 MET cc_start: 0.9089 (ttp) cc_final: 0.8857 (ttp) REVERT: C 1119 GLU cc_start: 0.7441 (pm20) cc_final: 0.6462 (tm-30) REVERT: B 438 ARG cc_start: 0.9015 (mtp-110) cc_final: 0.8803 (mtp-110) REVERT: B 457 MET cc_start: 0.8818 (mmm) cc_final: 0.8607 (mmm) REVERT: B 661 GLU cc_start: 0.8481 (pt0) cc_final: 0.8232 (pp20) REVERT: B 687 LEU cc_start: 0.9574 (tp) cc_final: 0.9274 (tp) REVERT: B 916 LEU cc_start: 0.9408 (mm) cc_final: 0.8976 (tt) REVERT: B 1124 PRO cc_start: 0.8499 (Cg_exo) cc_final: 0.8263 (Cg_endo) REVERT: B 1175 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8290 (mm-30) REVERT: B 1179 GLU cc_start: 0.8685 (tp30) cc_final: 0.8161 (tp30) REVERT: A 121 MET cc_start: 0.8199 (ptt) cc_final: 0.7675 (tmm) REVERT: A 138 MET cc_start: 0.7548 (ppp) cc_final: 0.7223 (ppp) REVERT: A 386 MET cc_start: 0.5792 (tpp) cc_final: 0.5368 (tpp) REVERT: A 407 LEU cc_start: 0.9342 (mm) cc_final: 0.8687 (tp) REVERT: A 935 MET cc_start: 0.8518 (tpt) cc_final: 0.8314 (tpt) REVERT: A 1026 MET cc_start: 0.8799 (tpp) cc_final: 0.8519 (tpp) REVERT: A 1178 ILE cc_start: 0.9573 (mm) cc_final: 0.9369 (mt) REVERT: D 134 LEU cc_start: 0.9332 (mp) cc_final: 0.9081 (mm) REVERT: D 138 MET cc_start: 0.9200 (mmm) cc_final: 0.8805 (mmm) REVERT: D 386 MET cc_start: 0.5050 (tpt) cc_final: 0.4813 (tpp) REVERT: D 479 MET cc_start: 0.8106 (pmm) cc_final: 0.7745 (pmm) REVERT: D 1085 ASN cc_start: 0.8853 (m-40) cc_final: 0.8449 (m110) REVERT: D 1207 MET cc_start: 0.8663 (mmp) cc_final: 0.8336 (mmm) outliers start: 71 outliers final: 40 residues processed: 498 average time/residue: 0.1712 time to fit residues: 144.1305 Evaluate side-chains 456 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 416 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 946 SER Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 1101 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 117 optimal weight: 8.9990 chunk 329 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 400 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 343 optimal weight: 20.0000 chunk 391 optimal weight: 0.7980 chunk 394 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 HIS ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1006 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.081403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.061656 restraints weight = 198443.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064769 restraints weight = 94734.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066787 restraints weight = 48405.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066982 restraints weight = 29093.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.067157 restraints weight = 28148.604| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32428 Z= 0.146 Angle : 0.651 10.904 44207 Z= 0.333 Chirality : 0.041 0.242 5144 Planarity : 0.005 0.072 5516 Dihedral : 6.515 59.616 5265 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.49 % Rotamer: Outliers : 2.59 % Allowed : 13.77 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 4081 helix: 0.37 (0.10), residues: 2569 sheet: -1.74 (0.34), residues: 234 loop : -2.03 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 438 TYR 0.026 0.001 TYR A 345 PHE 0.032 0.002 PHE C 854 TRP 0.030 0.002 TRP C 915 HIS 0.008 0.001 HIS B 723 Details of bonding type rmsd covalent geometry : bond 0.00319 (32424) covalent geometry : angle 0.65082 (44199) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.80159 ( 8) hydrogen bonds : bond 0.04519 ( 1804) hydrogen bonds : angle 4.78635 ( 5356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 445 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 HIS cc_start: 0.5464 (OUTLIER) cc_final: 0.4833 (p-80) REVERT: C 397 MET cc_start: 0.8437 (tpt) cc_final: 0.8169 (tpt) REVERT: C 444 TYR cc_start: 0.8410 (m-80) cc_final: 0.8040 (m-80) REVERT: C 558 PHE cc_start: 0.8655 (t80) cc_final: 0.8389 (t80) REVERT: C 688 ASP cc_start: 0.8673 (t70) cc_final: 0.8456 (t0) REVERT: C 699 MET cc_start: 0.8349 (mmt) cc_final: 0.8076 (mmt) REVERT: C 837 LEU cc_start: 0.9183 (mt) cc_final: 0.8965 (mm) REVERT: C 983 MET cc_start: 0.9026 (mmp) cc_final: 0.8579 (mmm) REVERT: C 1072 MET cc_start: 0.9124 (ttp) cc_final: 0.8884 (ttp) REVERT: C 1096 PHE cc_start: 0.8880 (t80) cc_final: 0.8622 (t80) REVERT: B 457 MET cc_start: 0.8850 (mmm) cc_final: 0.8532 (mmm) REVERT: B 625 MET cc_start: 0.7692 (ptp) cc_final: 0.7460 (ptp) REVERT: B 661 GLU cc_start: 0.8469 (pt0) cc_final: 0.8130 (pp20) REVERT: B 670 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8568 (mp10) REVERT: B 681 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8130 (tp40) REVERT: B 687 LEU cc_start: 0.9551 (tp) cc_final: 0.9249 (tp) REVERT: B 723 HIS cc_start: 0.8137 (t-90) cc_final: 0.7308 (t-90) REVERT: B 725 ASP cc_start: 0.7975 (p0) cc_final: 0.7743 (t0) REVERT: B 741 MET cc_start: 0.9024 (mmm) cc_final: 0.8191 (mtp) REVERT: B 747 ARG cc_start: 0.8351 (mmp-170) cc_final: 0.7907 (mmp-170) REVERT: B 916 LEU cc_start: 0.9381 (mm) cc_final: 0.8956 (tt) REVERT: B 967 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5851 (m-80) REVERT: B 1124 PRO cc_start: 0.8536 (Cg_exo) cc_final: 0.8307 (Cg_endo) REVERT: A 138 MET cc_start: 0.7549 (ppp) cc_final: 0.7204 (ppp) REVERT: A 386 MET cc_start: 0.5515 (tpp) cc_final: 0.5176 (tpp) REVERT: A 407 LEU cc_start: 0.9305 (mm) cc_final: 0.8607 (tp) REVERT: A 1026 MET cc_start: 0.8813 (tpp) cc_final: 0.8511 (tpp) REVERT: A 1132 HIS cc_start: 0.7470 (m170) cc_final: 0.7161 (m90) REVERT: D 138 MET cc_start: 0.9352 (mmm) cc_final: 0.8936 (mmp) REVERT: D 479 MET cc_start: 0.8087 (pmm) cc_final: 0.7685 (pmm) REVERT: D 1207 MET cc_start: 0.8658 (mmp) cc_final: 0.8311 (mmp) outliers start: 80 outliers final: 46 residues processed: 495 average time/residue: 0.1797 time to fit residues: 150.5255 Evaluate side-chains 450 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 400 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 670 GLN Chi-restraints excluded: chain B residue 681 GLN Chi-restraints excluded: chain B residue 714 CYS Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 946 SER Chi-restraints excluded: chain D residue 961 ILE Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 1101 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 187 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 290 optimal weight: 7.9990 chunk 353 optimal weight: 5.9990 chunk 198 optimal weight: 0.0670 chunk 16 optimal weight: 0.0270 chunk 278 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 364 optimal weight: 4.9990 chunk 407 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 HIS C 197 HIS ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.081852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.062244 restraints weight = 178866.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064473 restraints weight = 84916.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.065906 restraints weight = 51953.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.066852 restraints weight = 37255.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.067474 restraints weight = 29854.870| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32428 Z= 0.129 Angle : 0.637 12.481 44207 Z= 0.322 Chirality : 0.041 0.250 5144 Planarity : 0.004 0.069 5516 Dihedral : 6.265 59.087 5263 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.36 % Favored : 95.51 % Rotamer: Outliers : 2.62 % Allowed : 15.39 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.13), residues: 4081 helix: 0.63 (0.10), residues: 2573 sheet: -1.56 (0.34), residues: 236 loop : -1.96 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1203 TYR 0.026 0.001 TYR A 345 PHE 0.022 0.001 PHE A1001 TRP 0.029 0.001 TRP C 915 HIS 0.020 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00282 (32424) covalent geometry : angle 0.63749 (44199) SS BOND : bond 0.00159 ( 4) SS BOND : angle 0.67777 ( 8) hydrogen bonds : bond 0.04279 ( 1804) hydrogen bonds : angle 4.60080 ( 5356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 440 time to evaluate : 1.369 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: C 43 HIS cc_start: 0.5399 (OUTLIER) cc_final: 0.4809 (p-80) REVERT: C 136 HIS cc_start: 0.8839 (OUTLIER) cc_final: 0.8371 (m90) REVERT: C 444 TYR cc_start: 0.8424 (m-80) cc_final: 0.8060 (m-80) REVERT: C 492 TYR cc_start: 0.8128 (m-10) cc_final: 0.7917 (m-80) REVERT: C 558 PHE cc_start: 0.8560 (t80) cc_final: 0.8316 (t80) REVERT: C 688 ASP cc_start: 0.8662 (t70) cc_final: 0.8411 (t0) REVERT: C 699 MET cc_start: 0.8356 (mmt) cc_final: 0.8098 (mmt) REVERT: C 837 LEU cc_start: 0.9089 (mt) cc_final: 0.8849 (mm) REVERT: C 983 MET cc_start: 0.9007 (mmp) cc_final: 0.8617 (mmm) REVERT: C 994 MET cc_start: 0.9091 (tpt) cc_final: 0.8741 (tpt) REVERT: C 1072 MET cc_start: 0.9089 (ttp) cc_final: 0.8848 (ttp) REVERT: C 1096 PHE cc_start: 0.8888 (t80) cc_final: 0.8633 (t80) REVERT: B 459 ASP cc_start: 0.8799 (p0) cc_final: 0.8536 (p0) REVERT: B 625 MET cc_start: 0.7715 (ptp) cc_final: 0.7482 (ptp) REVERT: B 661 GLU cc_start: 0.8357 (pt0) cc_final: 0.8023 (pp20) REVERT: B 670 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8560 (mp10) REVERT: B 687 LEU cc_start: 0.9555 (tp) cc_final: 0.9275 (tp) REVERT: B 723 HIS cc_start: 0.8165 (t-90) cc_final: 0.7785 (t70) REVERT: B 741 MET cc_start: 0.9014 (mmm) cc_final: 0.8606 (mtp) REVERT: B 916 LEU cc_start: 0.9371 (mm) cc_final: 0.8954 (tt) REVERT: B 1124 PRO cc_start: 0.8468 (Cg_exo) cc_final: 0.8248 (Cg_endo) REVERT: A 138 MET cc_start: 0.7471 (ppp) cc_final: 0.7123 (ppp) REVERT: A 280 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 407 LEU cc_start: 0.9290 (mm) cc_final: 0.8564 (tp) REVERT: A 1026 MET cc_start: 0.8808 (tpp) cc_final: 0.8509 (tpp) REVERT: A 1132 HIS cc_start: 0.7458 (m170) cc_final: 0.7228 (m90) REVERT: A 1207 MET cc_start: 0.8715 (mmp) cc_final: 0.8365 (mmt) REVERT: D 138 MET cc_start: 0.9284 (mmm) cc_final: 0.8914 (mmp) REVERT: D 457 MET cc_start: 0.9196 (mmm) cc_final: 0.8871 (mmt) REVERT: D 479 MET cc_start: 0.8151 (pmm) cc_final: 0.7702 (pmm) REVERT: D 1026 MET cc_start: 0.8253 (mmm) cc_final: 0.7694 (mpp) outliers start: 81 outliers final: 53 residues processed: 487 average time/residue: 0.1692 time to fit residues: 140.9485 Evaluate side-chains 469 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 412 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1127 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 670 GLN Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1092 ASN Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 946 SER Chi-restraints excluded: chain D residue 961 ILE Chi-restraints excluded: chain D residue 969 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 57 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 267 optimal weight: 3.9990 chunk 359 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 374 optimal weight: 0.0570 chunk 225 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 overall best weight: 3.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 HIS ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN D1215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.079491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.060329 restraints weight = 153617.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.062319 restraints weight = 77705.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.063606 restraints weight = 49412.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.064459 restraints weight = 36478.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.064935 restraints weight = 29848.978| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32428 Z= 0.201 Angle : 0.688 16.213 44207 Z= 0.349 Chirality : 0.043 0.263 5144 Planarity : 0.005 0.069 5516 Dihedral : 6.279 58.074 5262 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.63 % Favored : 95.24 % Rotamer: Outliers : 3.21 % Allowed : 15.68 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4081 helix: 0.73 (0.10), residues: 2577 sheet: -1.50 (0.32), residues: 253 loop : -1.81 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1203 TYR 0.027 0.002 TYR A 345 PHE 0.035 0.002 PHE D 990 TRP 0.037 0.002 TRP C 915 HIS 0.031 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00442 (32424) covalent geometry : angle 0.68844 (44199) SS BOND : bond 0.00160 ( 4) SS BOND : angle 0.87008 ( 8) hydrogen bonds : bond 0.04416 ( 1804) hydrogen bonds : angle 4.67433 ( 5356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 410 time to evaluate : 1.197 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: C 43 HIS cc_start: 0.5519 (OUTLIER) cc_final: 0.4955 (p-80) REVERT: C 444 TYR cc_start: 0.8468 (m-80) cc_final: 0.8005 (m-80) REVERT: C 558 PHE cc_start: 0.8576 (t80) cc_final: 0.8349 (t80) REVERT: C 699 MET cc_start: 0.8311 (mmt) cc_final: 0.8108 (mmt) REVERT: C 724 ARG cc_start: 0.7829 (ttm110) cc_final: 0.7372 (tpp80) REVERT: C 837 LEU cc_start: 0.9166 (mt) cc_final: 0.8961 (mm) REVERT: C 979 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8586 (mtt) REVERT: C 983 MET cc_start: 0.9039 (mmp) cc_final: 0.8745 (mmm) REVERT: C 1096 PHE cc_start: 0.8939 (t80) cc_final: 0.8607 (t80) REVERT: B 457 MET cc_start: 0.8866 (mmm) cc_final: 0.8566 (mmm) REVERT: B 661 GLU cc_start: 0.8294 (pt0) cc_final: 0.7961 (pp20) REVERT: B 687 LEU cc_start: 0.9594 (tp) cc_final: 0.9339 (tp) REVERT: B 741 MET cc_start: 0.9046 (mmm) cc_final: 0.8723 (mtp) REVERT: B 916 LEU cc_start: 0.9389 (mm) cc_final: 0.8950 (tt) REVERT: B 984 MET cc_start: 0.8998 (mmm) cc_final: 0.8754 (tpp) REVERT: B 1175 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8340 (mm-30) REVERT: A 138 MET cc_start: 0.7492 (ppp) cc_final: 0.7133 (ppp) REVERT: A 279 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: A 280 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8227 (mm) REVERT: A 407 LEU cc_start: 0.9255 (mm) cc_final: 0.8518 (tp) REVERT: A 855 TYR cc_start: 0.8317 (t80) cc_final: 0.8007 (t80) REVERT: A 983 MET cc_start: 0.8966 (mmm) cc_final: 0.8729 (mmm) REVERT: A 1026 MET cc_start: 0.8841 (tpp) cc_final: 0.8548 (tpp) REVERT: A 1132 HIS cc_start: 0.7678 (m170) cc_final: 0.7405 (m90) REVERT: A 1179 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8389 (mp0) REVERT: A 1207 MET cc_start: 0.8683 (mmp) cc_final: 0.8338 (mmt) REVERT: D 43 HIS cc_start: 0.2219 (p-80) cc_final: -0.0168 (t70) REVERT: D 138 MET cc_start: 0.9374 (mmm) cc_final: 0.8995 (ptt) REVERT: D 457 MET cc_start: 0.9120 (mmm) cc_final: 0.8847 (mmt) REVERT: D 479 MET cc_start: 0.8250 (pmm) cc_final: 0.7739 (pmm) REVERT: D 1026 MET cc_start: 0.8369 (mmm) cc_final: 0.7811 (mpp) outliers start: 99 outliers final: 65 residues processed: 474 average time/residue: 0.1761 time to fit residues: 141.7295 Evaluate side-chains 457 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 387 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 1091 PHE Chi-restraints excluded: chain C residue 1127 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 714 CYS Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1097 GLU Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 961 ILE Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 1101 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 110 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 343 optimal weight: 9.9990 chunk 284 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 771 ASN ** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.078837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059481 restraints weight = 162284.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.061545 restraints weight = 79750.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.062879 restraints weight = 49877.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.063762 restraints weight = 36488.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.064337 restraints weight = 29627.512| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32428 Z= 0.201 Angle : 0.694 12.947 44207 Z= 0.352 Chirality : 0.042 0.242 5144 Planarity : 0.005 0.071 5516 Dihedral : 6.251 57.898 5261 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.68 % Favored : 95.19 % Rotamer: Outliers : 3.14 % Allowed : 16.33 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4081 helix: 0.78 (0.10), residues: 2584 sheet: -1.32 (0.31), residues: 265 loop : -1.77 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1203 TYR 0.024 0.001 TYR A 345 PHE 0.037 0.002 PHE D 931 TRP 0.040 0.002 TRP C 915 HIS 0.015 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00440 (32424) covalent geometry : angle 0.69334 (44199) SS BOND : bond 0.02048 ( 4) SS BOND : angle 1.73033 ( 8) hydrogen bonds : bond 0.04415 ( 1804) hydrogen bonds : angle 4.67198 ( 5356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 395 time to evaluate : 0.989 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: C 43 HIS cc_start: 0.5726 (OUTLIER) cc_final: 0.5141 (p-80) REVERT: C 179 MET cc_start: 0.9139 (mmp) cc_final: 0.8901 (mmp) REVERT: C 444 TYR cc_start: 0.8607 (m-80) cc_final: 0.8079 (m-80) REVERT: C 457 MET cc_start: 0.8606 (mmt) cc_final: 0.7847 (mmt) REVERT: C 558 PHE cc_start: 0.8644 (t80) cc_final: 0.8400 (t80) REVERT: C 699 MET cc_start: 0.8356 (mmt) cc_final: 0.8145 (mmt) REVERT: C 930 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8983 (tt) REVERT: C 983 MET cc_start: 0.9083 (mmp) cc_final: 0.8786 (mmm) REVERT: C 987 MET cc_start: 0.8758 (tpp) cc_final: 0.8461 (tpp) REVERT: C 1096 PHE cc_start: 0.9005 (t80) cc_final: 0.8679 (t80) REVERT: C 1221 MET cc_start: 0.8004 (mmp) cc_final: 0.7583 (mmp) REVERT: B 150 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8441 (mm) REVERT: B 661 GLU cc_start: 0.8348 (pt0) cc_final: 0.8029 (pp20) REVERT: B 687 LEU cc_start: 0.9575 (tp) cc_final: 0.9329 (tp) REVERT: B 693 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8260 (tm-30) REVERT: B 741 MET cc_start: 0.9136 (mmm) cc_final: 0.8387 (mtp) REVERT: B 747 ARG cc_start: 0.8338 (mmp-170) cc_final: 0.7986 (mmp-170) REVERT: B 916 LEU cc_start: 0.9417 (mm) cc_final: 0.8971 (tt) REVERT: B 984 MET cc_start: 0.9055 (mmm) cc_final: 0.8810 (tpp) REVERT: B 1175 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8380 (mm-30) REVERT: B 1207 MET cc_start: 0.8978 (mmp) cc_final: 0.8769 (mmm) REVERT: B 1221 MET cc_start: 0.8846 (ttp) cc_final: 0.8623 (mmp) REVERT: A 138 MET cc_start: 0.7476 (ppp) cc_final: 0.7161 (ppp) REVERT: A 280 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8462 (mm) REVERT: A 407 LEU cc_start: 0.9263 (mm) cc_final: 0.8526 (tp) REVERT: A 431 TRP cc_start: 0.8290 (m-10) cc_final: 0.7841 (m-90) REVERT: A 685 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8539 (mm-30) REVERT: A 1026 MET cc_start: 0.8836 (tpp) cc_final: 0.8469 (tpp) REVERT: A 1132 HIS cc_start: 0.7732 (m170) cc_final: 0.7509 (m90) REVERT: A 1207 MET cc_start: 0.8779 (mmp) cc_final: 0.8518 (mmt) REVERT: D 43 HIS cc_start: 0.2158 (p-80) cc_final: -0.0118 (t70) REVERT: D 138 MET cc_start: 0.9440 (mmm) cc_final: 0.9084 (ptt) REVERT: D 479 MET cc_start: 0.8379 (pmm) cc_final: 0.7814 (pmm) REVERT: D 1026 MET cc_start: 0.8428 (mmm) cc_final: 0.7732 (mpp) REVERT: D 1186 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8737 (p0) outliers start: 97 outliers final: 74 residues processed: 460 average time/residue: 0.1740 time to fit residues: 136.8507 Evaluate side-chains 451 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 372 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1091 PHE Chi-restraints excluded: chain C residue 1127 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 714 CYS Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 845 TYR Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 961 ILE Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1101 ILE Chi-restraints excluded: chain D residue 1186 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 150 optimal weight: 9.9990 chunk 394 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 363 optimal weight: 0.7980 chunk 320 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 285 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 ASN B1176 GLN ** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.078789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.059213 restraints weight = 178110.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.061362 restraints weight = 83799.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062752 restraints weight = 51414.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.063675 restraints weight = 37195.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.064188 restraints weight = 29936.027| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32428 Z= 0.188 Angle : 0.695 12.684 44207 Z= 0.350 Chirality : 0.042 0.238 5144 Planarity : 0.005 0.069 5516 Dihedral : 6.175 57.551 5260 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 2.69 % Allowed : 17.40 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4081 helix: 0.85 (0.10), residues: 2594 sheet: -0.95 (0.32), residues: 249 loop : -1.73 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1203 TYR 0.027 0.001 TYR A 345 PHE 0.028 0.002 PHE A 967 TRP 0.041 0.002 TRP C 915 HIS 0.006 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00419 (32424) covalent geometry : angle 0.69518 (44199) SS BOND : bond 0.00319 ( 4) SS BOND : angle 1.50963 ( 8) hydrogen bonds : bond 0.04370 ( 1804) hydrogen bonds : angle 4.65497 ( 5356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 387 time to evaluate : 1.240 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: C 43 HIS cc_start: 0.5668 (OUTLIER) cc_final: 0.5111 (p-80) REVERT: C 179 MET cc_start: 0.9112 (mmp) cc_final: 0.8848 (mmp) REVERT: C 444 TYR cc_start: 0.8622 (m-80) cc_final: 0.8051 (m-80) REVERT: C 457 MET cc_start: 0.8806 (mmt) cc_final: 0.8020 (mmt) REVERT: C 472 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8537 (tt) REVERT: C 558 PHE cc_start: 0.8674 (t80) cc_final: 0.8429 (t80) REVERT: C 699 MET cc_start: 0.8344 (mmt) cc_final: 0.8010 (mmt) REVERT: C 734 MET cc_start: 0.8560 (ppp) cc_final: 0.8215 (ppp) REVERT: C 930 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8993 (tt) REVERT: C 983 MET cc_start: 0.9083 (mmp) cc_final: 0.8802 (mmm) REVERT: C 1096 PHE cc_start: 0.9021 (t80) cc_final: 0.8680 (t80) REVERT: B 150 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8391 (mm) REVERT: B 661 GLU cc_start: 0.8339 (pt0) cc_final: 0.8009 (pp20) REVERT: B 687 LEU cc_start: 0.9596 (tp) cc_final: 0.9354 (tp) REVERT: B 693 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8203 (tm-30) REVERT: B 916 LEU cc_start: 0.9424 (mm) cc_final: 0.8985 (tt) REVERT: B 984 MET cc_start: 0.9061 (mmm) cc_final: 0.8801 (tpp) REVERT: B 1128 ILE cc_start: 0.9210 (tp) cc_final: 0.8920 (tp) REVERT: B 1175 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8624 (mm-30) REVERT: B 1221 MET cc_start: 0.8860 (ttp) cc_final: 0.8645 (mmp) REVERT: A 138 MET cc_start: 0.7606 (ppp) cc_final: 0.7302 (ppp) REVERT: A 280 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8414 (mm) REVERT: A 407 LEU cc_start: 0.9261 (mm) cc_final: 0.8508 (tp) REVERT: A 431 TRP cc_start: 0.8308 (m-10) cc_final: 0.7870 (m-90) REVERT: A 685 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8436 (mm-30) REVERT: A 1026 MET cc_start: 0.8826 (tpp) cc_final: 0.8461 (tpp) REVERT: A 1132 HIS cc_start: 0.7752 (m170) cc_final: 0.7542 (m90) REVERT: A 1207 MET cc_start: 0.8762 (mmp) cc_final: 0.8499 (mmt) REVERT: D 43 HIS cc_start: 0.2194 (p-80) cc_final: -0.0178 (t70) REVERT: D 138 MET cc_start: 0.9455 (mmm) cc_final: 0.9106 (ptt) REVERT: D 479 MET cc_start: 0.8421 (pmm) cc_final: 0.7815 (pmm) REVERT: D 1026 MET cc_start: 0.8397 (mmm) cc_final: 0.7784 (mpp) REVERT: D 1186 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8732 (p0) outliers start: 83 outliers final: 67 residues processed: 444 average time/residue: 0.1685 time to fit residues: 129.1409 Evaluate side-chains 443 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 370 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1091 PHE Chi-restraints excluded: chain C residue 1127 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 714 CYS Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1097 GLU Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 961 ILE Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1101 ILE Chi-restraints excluded: chain D residue 1186 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 266 optimal weight: 0.0970 chunk 285 optimal weight: 0.9990 chunk 225 optimal weight: 30.0000 chunk 198 optimal weight: 30.0000 chunk 161 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 400 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 319 optimal weight: 4.9990 chunk 123 optimal weight: 30.0000 chunk 311 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS ** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 733 GLN D1132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.080209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060634 restraints weight = 180338.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.062843 restraints weight = 85422.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.064262 restraints weight = 52289.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.065171 restraints weight = 37703.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.065694 restraints weight = 30302.533| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32428 Z= 0.133 Angle : 0.685 14.357 44207 Z= 0.337 Chirality : 0.041 0.353 5144 Planarity : 0.004 0.068 5516 Dihedral : 5.957 57.013 5260 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.71 % Rotamer: Outliers : 2.24 % Allowed : 18.08 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.13), residues: 4081 helix: 0.96 (0.10), residues: 2604 sheet: -0.94 (0.34), residues: 252 loop : -1.66 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1203 TYR 0.026 0.001 TYR A 345 PHE 0.031 0.002 PHE A 967 TRP 0.046 0.001 TRP C 915 HIS 0.005 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00295 (32424) covalent geometry : angle 0.68462 (44199) SS BOND : bond 0.00267 ( 4) SS BOND : angle 1.00941 ( 8) hydrogen bonds : bond 0.04142 ( 1804) hydrogen bonds : angle 4.48481 ( 5356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 421 time to evaluate : 1.289 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: C 43 HIS cc_start: 0.5409 (OUTLIER) cc_final: 0.4862 (p-80) REVERT: C 179 MET cc_start: 0.9022 (mmp) cc_final: 0.8775 (mmp) REVERT: C 444 TYR cc_start: 0.8536 (m-80) cc_final: 0.8051 (m-80) REVERT: C 457 MET cc_start: 0.8675 (mmt) cc_final: 0.8104 (mmt) REVERT: C 472 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8748 (tt) REVERT: C 558 PHE cc_start: 0.8559 (t80) cc_final: 0.8336 (t80) REVERT: C 699 MET cc_start: 0.8282 (mmt) cc_final: 0.8020 (mmt) REVERT: C 1030 MET cc_start: 0.8888 (mtp) cc_final: 0.8550 (mtp) REVERT: C 1096 PHE cc_start: 0.8937 (t80) cc_final: 0.8619 (t80) REVERT: C 1221 MET cc_start: 0.8163 (mmp) cc_final: 0.7770 (mmp) REVERT: B 150 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8426 (mm) REVERT: B 457 MET cc_start: 0.8805 (mmm) cc_final: 0.8513 (mtt) REVERT: B 661 GLU cc_start: 0.8330 (pt0) cc_final: 0.7924 (pp20) REVERT: B 687 LEU cc_start: 0.9573 (tp) cc_final: 0.9370 (tp) REVERT: B 916 LEU cc_start: 0.9409 (mm) cc_final: 0.8965 (tt) REVERT: B 1128 ILE cc_start: 0.9184 (tp) cc_final: 0.8893 (tp) REVERT: B 1175 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8555 (mm-30) REVERT: A 138 MET cc_start: 0.7414 (ppp) cc_final: 0.7135 (ppp) REVERT: A 280 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8430 (mm) REVERT: A 407 LEU cc_start: 0.9187 (mm) cc_final: 0.8443 (tp) REVERT: A 431 TRP cc_start: 0.8252 (m-10) cc_final: 0.7842 (m-90) REVERT: A 685 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8427 (mm-30) REVERT: A 1026 MET cc_start: 0.8780 (tpp) cc_final: 0.8443 (tpp) REVERT: A 1207 MET cc_start: 0.8739 (mmp) cc_final: 0.8403 (mmt) REVERT: D 43 HIS cc_start: 0.1790 (p-80) cc_final: -0.0349 (t70) REVERT: D 138 MET cc_start: 0.9370 (mmm) cc_final: 0.9098 (ptt) REVERT: D 337 ASP cc_start: 0.9150 (m-30) cc_final: 0.8835 (m-30) REVERT: D 479 MET cc_start: 0.8319 (pmm) cc_final: 0.7743 (pmm) REVERT: D 1026 MET cc_start: 0.8217 (mmm) cc_final: 0.7832 (mpp) REVERT: D 1030 MET cc_start: 0.8560 (mtp) cc_final: 0.7900 (mtp) outliers start: 69 outliers final: 56 residues processed: 466 average time/residue: 0.1765 time to fit residues: 141.4617 Evaluate side-chains 452 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 392 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1091 PHE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 961 ILE Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 1087 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 69 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 395 optimal weight: 0.0070 chunk 160 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 chunk 153 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 213 optimal weight: 9.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 ASN B 955 ASN ** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN D1132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.061434 restraints weight = 173128.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.063622 restraints weight = 83233.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.065009 restraints weight = 51309.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.065932 restraints weight = 37055.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.066469 restraints weight = 29703.955| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32428 Z= 0.126 Angle : 0.697 15.850 44207 Z= 0.340 Chirality : 0.042 0.394 5144 Planarity : 0.004 0.067 5516 Dihedral : 5.873 57.183 5260 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 1.85 % Allowed : 18.53 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 4081 helix: 1.00 (0.10), residues: 2606 sheet: -0.59 (0.35), residues: 235 loop : -1.65 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1203 TYR 0.028 0.001 TYR A 345 PHE 0.031 0.002 PHE A 967 TRP 0.050 0.001 TRP C 915 HIS 0.007 0.001 HIS A1132 Details of bonding type rmsd covalent geometry : bond 0.00277 (32424) covalent geometry : angle 0.69720 (44199) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.82084 ( 8) hydrogen bonds : bond 0.04022 ( 1804) hydrogen bonds : angle 4.44003 ( 5356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 424 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 HIS cc_start: 0.5287 (OUTLIER) cc_final: 0.4810 (p-80) REVERT: C 179 MET cc_start: 0.9014 (mmp) cc_final: 0.8788 (mmp) REVERT: C 444 TYR cc_start: 0.8511 (m-80) cc_final: 0.8054 (m-80) REVERT: C 457 MET cc_start: 0.8702 (mmt) cc_final: 0.8107 (mmt) REVERT: C 472 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8766 (tt) REVERT: C 558 PHE cc_start: 0.8538 (t80) cc_final: 0.8324 (t80) REVERT: C 699 MET cc_start: 0.8282 (mmt) cc_final: 0.8015 (mmt) REVERT: C 987 MET cc_start: 0.8414 (tpp) cc_final: 0.8060 (tmm) REVERT: C 1096 PHE cc_start: 0.8951 (t80) cc_final: 0.8640 (t80) REVERT: C 1180 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8068 (tm-30) REVERT: C 1221 MET cc_start: 0.8133 (mmp) cc_final: 0.7684 (mmt) REVERT: B 150 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8404 (mm) REVERT: B 179 MET cc_start: 0.8621 (mmm) cc_final: 0.8367 (mmp) REVERT: B 621 TRP cc_start: 0.8436 (t60) cc_final: 0.8209 (t60) REVERT: B 661 GLU cc_start: 0.8303 (pt0) cc_final: 0.7915 (pp20) REVERT: B 687 LEU cc_start: 0.9550 (tp) cc_final: 0.9305 (tp) REVERT: B 916 LEU cc_start: 0.9408 (mm) cc_final: 0.8959 (tt) REVERT: B 1128 ILE cc_start: 0.9235 (tp) cc_final: 0.8935 (tp) REVERT: B 1175 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8521 (mm-30) REVERT: A 138 MET cc_start: 0.7592 (ppp) cc_final: 0.7268 (ppp) REVERT: A 280 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8498 (mm) REVERT: A 407 LEU cc_start: 0.9166 (mm) cc_final: 0.8405 (tp) REVERT: A 431 TRP cc_start: 0.8226 (m-10) cc_final: 0.7860 (m-90) REVERT: A 539 LEU cc_start: 0.9566 (mt) cc_final: 0.9344 (tp) REVERT: A 685 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8328 (mm-30) REVERT: D 43 HIS cc_start: 0.1602 (p-80) cc_final: -0.0331 (t70) REVERT: D 138 MET cc_start: 0.9370 (mmm) cc_final: 0.9081 (ptt) REVERT: D 337 ASP cc_start: 0.9133 (m-30) cc_final: 0.8811 (m-30) REVERT: D 458 LEU cc_start: 0.9242 (tp) cc_final: 0.9021 (mt) REVERT: D 479 MET cc_start: 0.8314 (pmm) cc_final: 0.7767 (pmm) REVERT: D 1026 MET cc_start: 0.8199 (mmm) cc_final: 0.7788 (mpp) REVERT: D 1030 MET cc_start: 0.8550 (mtp) cc_final: 0.7885 (mtp) REVERT: D 1085 ASN cc_start: 0.8582 (m-40) cc_final: 0.8220 (m-40) outliers start: 57 outliers final: 43 residues processed: 456 average time/residue: 0.1706 time to fit residues: 134.4757 Evaluate side-chains 449 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 402 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 957 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 1087 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 47 optimal weight: 9.9990 chunk 289 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 263 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 255 optimal weight: 8.9990 chunk 202 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 267 optimal weight: 0.6980 chunk 349 optimal weight: 9.9990 chunk 297 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.081034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.061161 restraints weight = 189594.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064226 restraints weight = 93673.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065984 restraints weight = 47311.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066517 restraints weight = 30285.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.066560 restraints weight = 29049.215| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32428 Z= 0.129 Angle : 0.698 14.630 44207 Z= 0.341 Chirality : 0.042 0.249 5144 Planarity : 0.004 0.067 5516 Dihedral : 5.817 57.992 5260 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.34 % Favored : 95.54 % Rotamer: Outliers : 1.75 % Allowed : 18.76 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.13), residues: 4081 helix: 1.10 (0.10), residues: 2598 sheet: -0.50 (0.35), residues: 233 loop : -1.59 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1203 TYR 0.015 0.001 TYR A 958 PHE 0.030 0.002 PHE D 613 TRP 0.031 0.001 TRP C 915 HIS 0.008 0.001 HIS A1132 Details of bonding type rmsd covalent geometry : bond 0.00286 (32424) covalent geometry : angle 0.69807 (44199) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.69098 ( 8) hydrogen bonds : bond 0.03973 ( 1804) hydrogen bonds : angle 4.40578 ( 5356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6139.46 seconds wall clock time: 106 minutes 55.59 seconds (6415.59 seconds total)