Starting phenix.real_space_refine on Sun Jun 7 20:13:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r3d_53554/06_2026/9r3d_53554.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r3d_53554/06_2026/9r3d_53554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r3d_53554/06_2026/9r3d_53554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r3d_53554/06_2026/9r3d_53554.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r3d_53554/06_2026/9r3d_53554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r3d_53554/06_2026/9r3d_53554.map" } resolution = 3.12 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= 0.012 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: 5 Type Number sf(0) Gaussians P 197 5.49 5 S 162 5.16 5 C 25702 2.51 5 N 7499 2.21 5 O 8302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41862 Number of models: 1 Model: "" Number of chains: 18 Chain: "5" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1620 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 4, 'rna3p_pur': 24, 'rna3p_pyr': 40} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "6" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1821 Classifications: {'RNA': 85} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 44, 'rna3p_pyr': 27} Link IDs: {'rna2p': 13, 'rna3p': 71} Chain: "B" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 4369 Classifications: {'peptide': 868} Incomplete info: {'truncation_to_alanine': 733} Link IDs: {'PTRANS': 38, 'TRANS': 829} Unresolved non-hydrogen bonds: 2734 Unresolved non-hydrogen angles: 3488 Unresolved non-hydrogen dihedrals: 2248 Unresolved non-hydrogen chiralities: 276 Planarities with less than four sites: {'HIS:plan': 24, 'PHE:plan': 35, 'ASN:plan1': 30, 'ARG:plan': 48, 'GLN:plan1': 39, 'ASP:plan': 42, 'TYR:plan': 29, 'GLU:plan': 69, 'TRP:plan': 9} Unresolved non-hydrogen planarities: 1502 Chain: "C" Number of atoms: 6649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6649 Classifications: {'peptide': 843} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 793} Chain: "I" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1521 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "K" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 940 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 3, 'GLU:plan': 15, 'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 147 Chain: "Q" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1173 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "T" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1691 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 2, 'TRANS': 221} Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 8, 'PHE:plan': 2, 'ARG:plan': 6, 'GLU:plan': 5, 'TYR:plan': 3, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 127 Chain: "X" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 291 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "Z" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 619 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 9, 'rna3p': 19} Chain: "q" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 599 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "r" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 728 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "P7" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 92 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 16} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 17219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2208, 17212 Classifications: {'peptide': 2208} Incomplete info: {'truncation_to_alanine': 310} Link IDs: {'PCIS': 3, 'PTRANS': 121, 'TRANS': 2083} Chain breaks: 4 Unresolved non-hydrogen bonds: 1158 Unresolved non-hydrogen angles: 1496 Unresolved non-hydrogen dihedrals: 964 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLU:plan': 23, 'PHE:plan': 15, 'ASN:plan1': 17, 'GLN:plan1': 19, 'TRP:plan': 9, 'ASP:plan': 20, 'TYR:plan': 11, 'ARG:plan': 13, 'HIS:plan': 9} Unresolved non-hydrogen planarities: 637 Conformer: "B" Number of residues, atoms: 2208, 17212 Classifications: {'peptide': 2208} Incomplete info: {'truncation_to_alanine': 310} Link IDs: {'PCIS': 3, 'PTRANS': 121, 'TRANS': 2083} Chain breaks: 4 Unresolved non-hydrogen bonds: 1158 Unresolved non-hydrogen angles: 1496 Unresolved non-hydrogen dihedrals: 964 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLU:plan': 23, 'PHE:plan': 15, 'ASN:plan1': 17, 'GLN:plan1': 19, 'TRP:plan': 9, 'ASP:plan': 20, 'TYR:plan': 11, 'ARG:plan': 13, 'HIS:plan': 9} Unresolved non-hydrogen planarities: 637 bond proxies already assigned to first conformer: 17658 Chain: "P" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1309 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 12, 'TRANS': 148} Chain breaks: 1 Chain: "t" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain breaks: 1 Chain: "S1" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 524 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain breaks: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 5, 'GLN:plan1': 4, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.52, per 1000 atoms: 0.30 Number of scatterers: 41862 At special positions: 0 Unit cell: (199.8, 234.9, 183.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 162 16.00 P 197 15.00 O 8302 8.00 N 7499 7.00 C 25702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 3.73 Conformation dependent library (CDL) restraints added in 2.3 seconds 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9806 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 35 sheets defined 49.4% alpha, 8.7% beta 37 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 482 through 495 Processing helix chain 'B' and resid 509 through 525 removed outlier: 3.967A pdb=" N MET B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 529 Processing helix chain 'B' and resid 544 through 562 removed outlier: 4.242A pdb=" N LYS B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 582 removed outlier: 4.004A pdb=" N ILE B 580 " --> pdb=" O CYS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 600 removed outlier: 3.712A pdb=" N GLY B 600 " --> pdb=" O ILE B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 removed outlier: 4.142A pdb=" N THR B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 635 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 659 through 666 Processing helix chain 'B' and resid 696 through 715 Processing helix chain 'B' and resid 729 through 748 removed outlier: 3.711A pdb=" N ALA B 735 " --> pdb=" O THR B 731 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE B 738 " --> pdb=" O THR B 734 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 747 " --> pdb=" O LEU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 758 removed outlier: 3.820A pdb=" N SER B 758 " --> pdb=" O GLY B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 768 Processing helix chain 'B' and resid 791 through 803 removed outlier: 4.899A pdb=" N GLU B 798 " --> pdb=" O ARG B 794 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP B 799 " --> pdb=" O THR B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 820 removed outlier: 3.549A pdb=" N VAL B 819 " --> pdb=" O LEU B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 855 Processing helix chain 'B' and resid 874 through 880 Processing helix chain 'B' and resid 885 through 891 removed outlier: 4.102A pdb=" N ILE B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 908 Processing helix chain 'B' and resid 909 through 911 No H-bonds generated for 'chain 'B' and resid 909 through 911' Processing helix chain 'B' and resid 913 through 936 removed outlier: 4.964A pdb=" N GLY B 921 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR B 922 " --> pdb=" O ASN B 918 " (cutoff:3.500A) Proline residue: B 933 - end of helix Processing helix chain 'B' and resid 938 through 944 Processing helix chain 'B' and resid 949 through 954 Processing helix chain 'B' and resid 954 through 982 removed outlier: 4.046A pdb=" N ASP B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS B 974 " --> pdb=" O VAL B 970 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN B 978 " --> pdb=" O LYS B 974 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE B 979 " --> pdb=" O LYS B 975 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 991 Processing helix chain 'B' and resid 994 through 1005 Processing helix chain 'B' and resid 1010 through 1021 Processing helix chain 'B' and resid 1033 through 1043 Processing helix chain 'B' and resid 1054 through 1069 Processing helix chain 'B' and resid 1074 through 1102 removed outlier: 4.280A pdb=" N GLY B1089 " --> pdb=" O THR B1085 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG B1090 " --> pdb=" O GLN B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1121 Processing helix chain 'B' and resid 1127 through 1132 removed outlier: 3.952A pdb=" N GLN B1131 " --> pdb=" O PRO B1128 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1146 Processing helix chain 'B' and resid 1157 through 1166 Processing helix chain 'B' and resid 1167 through 1181 removed outlier: 4.388A pdb=" N LYS B1172 " --> pdb=" O PRO B1168 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N THR B1173 " --> pdb=" O LYS B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1216 removed outlier: 4.128A pdb=" N GLY B1216 " --> pdb=" O GLU B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1242 through 1247 removed outlier: 4.017A pdb=" N GLN B1247 " --> pdb=" O ALA B1243 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 125 removed outlier: 3.591A pdb=" N ASN C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 154 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 211 through 222 removed outlier: 4.200A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 260 through 266 removed outlier: 3.900A pdb=" N ILE C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 Processing helix chain 'C' and resid 321 through 331 Processing helix chain 'C' and resid 335 through 342 removed outlier: 3.705A pdb=" N LYS C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 387 Processing helix chain 'C' and resid 391 through 400 Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.617A pdb=" N LYS C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 438 removed outlier: 3.572A pdb=" N VAL C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 5.070A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 Processing helix chain 'C' and resid 633 through 647 Processing helix chain 'C' and resid 695 through 702 removed outlier: 3.535A pdb=" N ASP C 699 " --> pdb=" O GLY C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 721 removed outlier: 4.515A pdb=" N LYS C 721 " --> pdb=" O PHE C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 removed outlier: 4.082A pdb=" N ARG C 730 " --> pdb=" O LEU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 777 removed outlier: 4.447A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 803 Processing helix chain 'C' and resid 804 through 823 Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 839 through 841 No H-bonds generated for 'chain 'C' and resid 839 through 841' Processing helix chain 'C' and resid 842 through 853 Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 928 through 941 Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 22 through 31 Processing helix chain 'I' and resid 32 through 38 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 68 through 81 Processing helix chain 'I' and resid 83 through 93 Processing helix chain 'I' and resid 96 through 110 Processing helix chain 'I' and resid 112 through 120 Processing helix chain 'I' and resid 121 through 126 removed outlier: 3.845A pdb=" N ASN I 125 " --> pdb=" O PRO I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 154 Processing helix chain 'I' and resid 167 through 174 Processing helix chain 'K' and resid 272 through 318 removed outlier: 4.710A pdb=" N LYS K 301 " --> pdb=" O LEU K 297 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE K 304 " --> pdb=" O GLU K 300 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG K 316 " --> pdb=" O GLU K 312 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA K 317 " --> pdb=" O GLU K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 353 through 357 Processing helix chain 'K' and resid 364 through 369 removed outlier: 3.502A pdb=" N HIS K 368 " --> pdb=" O LEU K 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 375 through 379 Processing helix chain 'K' and resid 393 through 398 Processing helix chain 'Q' and resid 14 through 34 Proline residue: Q 20 - end of helix Processing helix chain 'Q' and resid 41 through 65 Proline residue: Q 48 - end of helix Processing helix chain 'Q' and resid 71 through 81 Processing helix chain 'Q' and resid 85 through 94 removed outlier: 3.602A pdb=" N LYS Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 106 removed outlier: 3.831A pdb=" N ILE Q 106 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 111 removed outlier: 3.614A pdb=" N ASP Q 110 " --> pdb=" O GLN Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 121 Processing helix chain 'T' and resid 858 through 910 removed outlier: 4.056A pdb=" N ALA T 879 " --> pdb=" O GLU T 875 " (cutoff:3.500A) Processing helix chain 'T' and resid 917 through 927 removed outlier: 3.682A pdb=" N THR T 921 " --> pdb=" O SER T 917 " (cutoff:3.500A) Processing helix chain 'T' and resid 931 through 936 Processing helix chain 'T' and resid 938 through 967 Processing helix chain 'T' and resid 977 through 984 Processing helix chain 'T' and resid 987 through 993 Processing helix chain 'T' and resid 1000 through 1037 removed outlier: 3.958A pdb=" N LYS T1016 " --> pdb=" O TYR T1012 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA T1017 " --> pdb=" O ILE T1013 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE T1029 " --> pdb=" O GLU T1025 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS T1035 " --> pdb=" O TYR T1031 " (cutoff:3.500A) Processing helix chain 'T' and resid 1039 through 1054 removed outlier: 3.693A pdb=" N HIS T1043 " --> pdb=" O GLU T1039 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP T1054 " --> pdb=" O ILE T1050 " (cutoff:3.500A) Processing helix chain 'T' and resid 1063 through 1080 removed outlier: 3.519A pdb=" N ARG T1067 " --> pdb=" O VAL T1063 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 48 removed outlier: 3.643A pdb=" N LYS X 48 " --> pdb=" O VAL X 44 " (cutoff:3.500A) Processing helix chain 'q' and resid 23 through 36 Processing helix chain 'q' and resid 38 through 40 No H-bonds generated for 'chain 'q' and resid 38 through 40' Processing helix chain 'q' and resid 56 through 61 Processing helix chain 'r' and resid 73 through 77 Processing helix chain 'r' and resid 91 through 100 Processing helix chain 'r' and resid 101 through 108 Processing helix chain 'r' and resid 118 through 133 Processing helix chain 'P7' and resid 124 through 131 removed outlier: 3.748A pdb=" N ARGP7 129 " --> pdb=" O PHEP7 125 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARGP7 130 " --> pdb=" O GLUP7 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.744A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.033A pdb=" N TYR A 254 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.539A pdb=" N ASP A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 395 through 405 removed outlier: 4.075A pdb=" N ALA A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.896A pdb=" N LEU A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.604A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 460 Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.746A pdb=" N THR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 541 through 566 Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.707A pdb=" N TYR A 594 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 596 No H-bonds generated for 'chain 'A' and resid 595 through 596' Processing helix chain 'A' and resid 597 through 617 removed outlier: 4.252A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 661 Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 678 through 697 removed outlier: 4.282A pdb=" N ASP A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 702 removed outlier: 3.633A pdb=" N ILE A 701 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 702 " --> pdb=" O GLU A 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 698 through 702' Processing helix chain 'A' and resid 705 through 723 Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 797 Processing helix chain 'A' and resid 802 through 820 Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 857 through 873 removed outlier: 4.228A pdb=" N GLU A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 873 " --> pdb=" O GLN A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 887 removed outlier: 4.028A pdb=" N ALA A 877 " --> pdb=" O ASN A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 933 removed outlier: 3.561A pdb=" N ARG A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 962 Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.608A pdb=" N ILE A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1014 Processing helix chain 'A' and resid 1036 through 1054 Processing helix chain 'A' and resid 1054 through 1063 removed outlier: 3.579A pdb=" N ALA A1058 " --> pdb=" O GLY A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1082 Processing helix chain 'A' and resid 1102 through 1117 Processing helix chain 'A' and resid 1143 through 1160 Processing helix chain 'A' and resid 1169 through 1173 Processing helix chain 'A' and resid 1233 through 1249 Processing helix chain 'A' and resid 1255 through 1272 Processing helix chain 'A' and resid 1281 through 1304 Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 4.306A pdb=" N PHE A1316 " --> pdb=" O PRO A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1336 through 1339 Processing helix chain 'A' and resid 1367 through 1372 Processing helix chain 'A' and resid 1374 through 1400 Processing helix chain 'A' and resid 1405 through 1412 removed outlier: 4.068A pdb=" N GLU A1409 " --> pdb=" O GLU A1406 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASP A1410 " --> pdb=" O ASP A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1435 through 1443 Processing helix chain 'A' and resid 1444 through 1446 No H-bonds generated for 'chain 'A' and resid 1444 through 1446' Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'A' and resid 1467 through 1479 Processing helix chain 'A' and resid 1479 through 1488 removed outlier: 4.001A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A1488 " --> pdb=" O ILE A1484 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1494 Processing helix chain 'A' and resid 1531 through 1538 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1575 Processing helix chain 'A' and resid 1580 through 1599 Processing helix chain 'A' and resid 1615 through 1621 removed outlier: 4.174A pdb=" N SER A1619 " --> pdb=" O PRO A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1688 Processing helix chain 'A' and resid 1721 through 1736 removed outlier: 3.716A pdb=" N LEU A1725 " --> pdb=" O GLY A1721 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1795 through 1799 removed outlier: 4.141A pdb=" N LEU A1798 " --> pdb=" O GLU A1795 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A1799 " --> pdb=" O GLY A1796 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1795 through 1799' Processing helix chain 'A' and resid 1831 through 1851 Processing helix chain 'A' and resid 1868 through 1879 removed outlier: 4.446A pdb=" N HIS A1875 " --> pdb=" O PRO A1871 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1876 " --> pdb=" O LEU A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1896 through 1908 removed outlier: 4.293A pdb=" N PHE A1902 " --> pdb=" O LYS A1898 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP A1904 " --> pdb=" O GLU A1900 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1946 Processing helix chain 'A' and resid 1946 through 1953 Processing helix chain 'A' and resid 1972 through 1995 Processing helix chain 'A' and resid 2003 through 2010 Processing helix chain 'A' and resid 2073 through 2087 Processing helix chain 'A' and resid 2107 through 2117 Processing helix chain 'A' and resid 2166 through 2172 Processing helix chain 'A' and resid 2189 through 2203 Processing helix chain 'A' and resid 2234 through 2240 removed outlier: 4.298A pdb=" N GLY A2238 " --> pdb=" O GLY A2234 " (cutoff:3.500A) Processing helix chain 'A' and resid 2252 through 2256 Processing helix chain 'A' and resid 2281 through 2285 Processing helix chain 'A' and resid 2312 through 2320 removed outlier: 3.502A pdb=" N ALA A2318 " --> pdb=" O PHE A2314 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 29 removed outlier: 3.682A pdb=" N LEU P 28 " --> pdb=" O CYS P 24 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY P 29 " --> pdb=" O GLN P 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 24 through 29' Processing helix chain 'P' and resid 71 through 78 removed outlier: 3.721A pdb=" N LYS P 78 " --> pdb=" O CYS P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 99 removed outlier: 3.580A pdb=" N ARG P 97 " --> pdb=" O PRO P 93 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 150 Processing helix chain 'P' and resid 156 through 161 removed outlier: 3.708A pdb=" N ARG P 161 " --> pdb=" O LYS P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 170 removed outlier: 3.627A pdb=" N LYS P 170 " --> pdb=" O SER P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 179 Processing helix chain 'P' and resid 198 through 204 Processing helix chain 'P' and resid 207 through 220 Processing helix chain 't' and resid 62 through 73 removed outlier: 3.670A pdb=" N ILE t 66 " --> pdb=" O ASP t 62 " (cutoff:3.500A) Proline residue: t 68 - end of helix Processing helix chain 't' and resid 127 through 139 removed outlier: 4.215A pdb=" N VAL t 131 " --> pdb=" O ALA t 127 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE t 136 " --> pdb=" O GLU t 132 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS t 137 " --> pdb=" O GLN t 133 " (cutoff:3.500A) Processing helix chain 'S1' and resid 283 through 324 removed outlier: 3.536A pdb=" N ARGS1 296 " --> pdb=" O TYRS1 292 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARGS1 299 " --> pdb=" O ASPS1 295 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HISS1 320 " --> pdb=" O GLUS1 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 688 through 690 removed outlier: 7.308A pdb=" N ILE B 828 " --> pdb=" O ILE B 870 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1189 through 1191 removed outlier: 3.596A pdb=" N HIS B1189 " --> pdb=" O GLU B1201 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B1200 " --> pdb=" O PHE B1254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1233 through 1236 removed outlier: 8.111A pdb=" N ILE B1233 " --> pdb=" O ASP B1227 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP B1227 " --> pdb=" O ILE B1233 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE B1221 " --> pdb=" O PHE B1239 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B1239 " --> pdb=" O PHE B1221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1233 through 1236 removed outlier: 8.111A pdb=" N ILE B1233 " --> pdb=" O ASP B1227 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP B1227 " --> pdb=" O ILE B1233 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B1270 " --> pdb=" O THR B1280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 184 through 191 removed outlier: 6.526A pdb=" N ARG C 130 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N MET C 203 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL C 132 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL C 225 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N CYS C 256 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU C 227 " --> pdb=" O CYS C 256 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN C 258 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE C 229 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N CYS C 308 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 348 through 350 removed outlier: 3.536A pdb=" N LYS C 355 " --> pdb=" O ASN C 350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.515A pdb=" N PHE C 493 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET C 481 " --> pdb=" O HIS C 491 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N HIS C 491 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AA9, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.624A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.624A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 663 through 666 removed outlier: 6.954A pdb=" N THR C 870 " --> pdb=" O ASP C 860 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP C 860 " --> pdb=" O THR C 870 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LYS C 872 " --> pdb=" O THR C 858 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 663 through 666 removed outlier: 6.833A pdb=" N LEU C 827 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE C 906 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLU C 829 " --> pdb=" O TRP C 904 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TRP C 904 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR C 831 " --> pdb=" O HIS C 902 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 898 " --> pdb=" O GLU C 835 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 674 through 677 removed outlier: 6.508A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE C 744 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE C 791 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C 746 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ASP C 793 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 57 through 58 Processing sheet with id=AB6, first strand: chain 'I' and resid 60 through 61 Processing sheet with id=AB7, first strand: chain 'I' and resid 156 through 157 Processing sheet with id=AB8, first strand: chain 'q' and resid 13 through 18 removed outlier: 8.656A pdb=" N LEU q 68 " --> pdb=" O GLU q 3 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL q 5 " --> pdb=" O LEU q 68 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU q 70 " --> pdb=" O VAL q 5 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN q 7 " --> pdb=" O LEU q 70 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N TYR q 72 " --> pdb=" O ASN q 7 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'r' and resid 65 through 67 Processing sheet with id=AC1, first strand: chain 'r' and resid 80 through 82 Processing sheet with id=AC2, first strand: chain 'P7' and resid 115 through 117 Processing sheet with id=AC3, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AC4, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AC5, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AC6, first strand: chain 'A' and resid 516 through 519 removed outlier: 3.550A pdb=" N ASP A 519 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 897 through 900 Processing sheet with id=AC8, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 6.692A pdb=" N PHE A1098 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A1088 " --> pdb=" O HIS A1096 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N HIS A1096 " --> pdb=" O PHE A1088 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG A1090 " --> pdb=" O ARG A1094 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A1094 " --> pdb=" O ARG A1090 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1016 through 1017 Processing sheet with id=AD1, first strand: chain 'A' and resid 1185 through 1189 Processing sheet with id=AD2, first strand: chain 'A' and resid 1341 through 1345 Processing sheet with id=AD3, first strand: chain 'A' and resid 1501 through 1503 removed outlier: 3.789A pdb=" N TYR A1754 " --> pdb=" O PHE A1502 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1553 through 1554 Processing sheet with id=AD5, first strand: chain 'A' and resid 1643 through 1644 removed outlier: 6.529A pdb=" N GLN A1658 " --> pdb=" O ALA A1633 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2104 through 2105 Processing sheet with id=AD7, first strand: chain 'A' and resid 2216 through 2217 removed outlier: 7.053A pdb=" N CYS A2216 " --> pdb=" O TRP A2177 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N HIS A2179 " --> pdb=" O CYS A2216 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR A2127 " --> pdb=" O VAL A2146 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A2146 " --> pdb=" O TYR A2127 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE A2145 " --> pdb=" O MET A2272 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2151 through 2152 removed outlier: 4.077A pdb=" N TRP A2151 " --> pdb=" O HIS A2158 " (cutoff:3.500A) 1866 hydrogen bonds defined for protein. 5310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 12.90 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13253 1.34 - 1.46: 7254 1.46 - 1.58: 21993 1.58 - 1.69: 385 1.69 - 1.81: 254 Bond restraints: 43139 Sorted by residual: bond pdb=" O12 IHP A2401 " pdb=" P2 IHP A2401 " ideal model delta sigma weight residual 1.675 1.605 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O16 IHP A2401 " pdb=" P6 IHP A2401 " ideal model delta sigma weight residual 1.672 1.604 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O14 IHP A2401 " pdb=" P4 IHP A2401 " ideal model delta sigma weight residual 1.671 1.604 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O15 IHP A2401 " pdb=" P5 IHP A2401 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O13 IHP A2401 " pdb=" P3 IHP A2401 " ideal model delta sigma weight residual 1.669 1.612 0.057 2.00e-02 2.50e+03 8.17e+00 ... (remaining 43134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 58964 2.00 - 4.00: 578 4.00 - 5.99: 71 5.99 - 7.99: 13 7.99 - 9.99: 5 Bond angle restraints: 59631 Sorted by residual: angle pdb=" N GLU A 684 " pdb=" CA GLU A 684 " pdb=" CB GLU A 684 " ideal model delta sigma weight residual 110.28 115.65 -5.37 1.55e+00 4.16e-01 1.20e+01 angle pdb=" N GLU T 886 " pdb=" CA GLU T 886 " pdb=" CB GLU T 886 " ideal model delta sigma weight residual 110.16 115.03 -4.87 1.48e+00 4.57e-01 1.08e+01 angle pdb=" N ASP C 638 " pdb=" CA ASP C 638 " pdb=" C ASP C 638 " ideal model delta sigma weight residual 111.40 107.40 4.00 1.22e+00 6.72e-01 1.07e+01 angle pdb=" C1 IHP A2401 " pdb=" C2 IHP A2401 " pdb=" C3 IHP A2401 " ideal model delta sigma weight residual 108.51 118.19 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB MET A 690 " pdb=" CG MET A 690 " pdb=" SD MET A 690 " ideal model delta sigma weight residual 112.70 122.01 -9.31 3.00e+00 1.11e-01 9.63e+00 ... (remaining 59626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.13: 24906 30.13 - 60.27: 1120 60.27 - 90.40: 219 90.40 - 120.54: 9 120.54 - 150.67: 2 Dihedral angle restraints: 26256 sinusoidal: 11167 harmonic: 15089 Sorted by residual: dihedral pdb=" CA ASN A1018 " pdb=" C ASN A1018 " pdb=" N TYR A1019 " pdb=" CA TYR A1019 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" C4 IHP A2401 " pdb=" C2 IHP A2401 " pdb=" C3 IHP A2401 " pdb=" O12 IHP A2401 " ideal model delta sinusoidal sigma weight residual 60.90 -148.43 -150.67 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" C6 IHP A2401 " pdb=" C1 IHP A2401 " pdb=" C2 IHP A2401 " pdb=" O12 IHP A2401 " ideal model delta sinusoidal sigma weight residual 61.05 -154.75 -144.20 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 26253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.989: 6892 0.989 - 1.978: 0 1.978 - 2.967: 0 2.967 - 3.955: 0 3.955 - 4.944: 4 Chirality restraints: 6896 Sorted by residual: chirality pdb=" C2 IHP A2401 " pdb=" C1 IHP A2401 " pdb=" C3 IHP A2401 " pdb=" O12 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.52 2.43 -4.94 2.00e-01 2.50e+01 6.11e+02 chirality pdb=" C5 IHP A2401 " pdb=" C4 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" O15 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.42 2.41 -4.83 2.00e-01 2.50e+01 5.83e+02 chirality pdb=" C1 IHP A2401 " pdb=" C2 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" O11 IHP A2401 " both_signs ideal model delta sigma weight residual False 2.32 -2.38 4.70 2.00e-01 2.50e+01 5.52e+02 ... (remaining 6893 not shown) Planarity restraints: 7103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 724 " -0.022 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP C 724 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C 724 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 724 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 724 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 724 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 724 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 724 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 724 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 724 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 828 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.92e+00 pdb=" N PRO A 829 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 829 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 829 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP T 931 " -0.020 2.00e-02 2.50e+03 1.50e-02 5.63e+00 pdb=" CG TRP T 931 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP T 931 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP T 931 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP T 931 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP T 931 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP T 931 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 931 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 931 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP T 931 " -0.000 2.00e-02 2.50e+03 ... (remaining 7100 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4522 2.75 - 3.29: 41960 3.29 - 3.82: 74344 3.82 - 4.36: 84892 4.36 - 4.90: 139191 Nonbonded interactions: 344909 Sorted by model distance: nonbonded pdb=" O PRO A1724 " pdb=" NE2 GLN A1728 " model vdw 2.209 3.120 nonbonded pdb=" OE1 GLU A1607 " pdb=" OG1 THR A1608 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A1091 " pdb=" OD2 ASP A1441 " model vdw 2.229 3.040 nonbonded pdb=" O TRP A 720 " pdb=" NZ LYS A 785 " model vdw 2.230 3.120 nonbonded pdb=" NH2 ARG A 934 " pdb=" O PRO A1065 " model vdw 2.234 3.120 ... (remaining 344904 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 50.840 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 43139 Z= 0.118 Angle : 0.500 9.991 59631 Z= 0.259 Chirality : 0.122 4.944 6896 Planarity : 0.003 0.075 7103 Dihedral : 16.881 150.670 16450 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.75 (0.12), residues: 5104 helix: 1.60 (0.11), residues: 2238 sheet: -0.50 (0.24), residues: 480 loop : -0.29 (0.13), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 870 TYR 0.021 0.001 TYR C 831 PHE 0.011 0.001 PHE t 61 TRP 0.054 0.002 TRP C 724 HIS 0.005 0.001 HIS A1580 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (43139) covalent geometry : angle 0.49971 / 0.26 (59631) hydrogen bonds : bond 0.16521 / 9.89 ( 1940) hydrogen bonds : angle 6.69478 / 3.98 ( 5464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 993 PHE cc_start: 0.2275 (m-80) cc_final: 0.1949 (m-80) REVERT: q 1 MET cc_start: 0.7202 (ptm) cc_final: 0.6921 (ptp) REVERT: q 7 ASN cc_start: 0.9088 (t0) cc_final: 0.8689 (t0) REVERT: r 68 ILE cc_start: 0.5837 (mm) cc_final: 0.5475 (mm) REVERT: A 1268 ILE cc_start: 0.8360 (mm) cc_final: 0.8129 (mm) REVERT: A 1686 ASP cc_start: 0.7473 (t0) cc_final: 0.7092 (t0) REVERT: A 1734 MET cc_start: 0.6863 (ttm) cc_final: 0.6548 (ttm) REVERT: A 2046 THR cc_start: 0.8095 (t) cc_final: 0.7870 (t) outliers start: 0 outliers final: 0 residues processed: 631 average time/residue: 0.2687 time to fit residues: 274.9483 Evaluate side-chains 556 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 0.8980 chunk 41 optimal weight: 40.0000 chunk 265 optimal weight: 0.2980 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 8.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN C 411 ASN ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN C 924 GLN I 166 GLN Q 55 GLN X 20 GLN A1069 ASN A1238 GLN A1296 GLN ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1420 ASN ** A2288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 GLN ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.174865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.140050 restraints weight = 88840.136| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.34 r_work: 0.3483 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43139 Z= 0.136 Angle : 0.575 27.647 59631 Z= 0.283 Chirality : 0.047 1.596 6896 Planarity : 0.004 0.061 7103 Dihedral : 15.214 114.477 8482 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.61 % Favored : 97.37 % Rotamer: Outliers : 0.73 % Allowed : 7.42 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.69 (0.12), residues: 5104 helix: 1.50 (0.11), residues: 2293 sheet: -0.66 (0.23), residues: 480 loop : -0.29 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1090 TYR 0.024 0.001 TYR C 831 PHE 0.015 0.001 PHE C 339 TRP 0.030 0.001 TRP T 931 HIS 0.007 0.001 HIS A1580 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (43139) covalent geometry : angle 0.57532 / 0.28 (59631) hydrogen bonds : bond 0.04577 / 2.72 ( 1940) hydrogen bonds : angle 4.99774 / 2.99 ( 5464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 588 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 699 ASP cc_start: 0.7458 (m-30) cc_final: 0.7234 (m-30) REVERT: C 829 GLU cc_start: 0.8169 (pt0) cc_final: 0.7966 (pt0) REVERT: I 85 ASP cc_start: 0.7773 (p0) cc_final: 0.7390 (p0) REVERT: I 146 GLU cc_start: 0.7766 (pm20) cc_final: 0.7269 (pm20) REVERT: T 927 LYS cc_start: 0.5780 (ttmm) cc_final: 0.5256 (tptm) REVERT: T 944 LYS cc_start: 0.7483 (tttt) cc_final: 0.6972 (ptmm) REVERT: T 993 PHE cc_start: 0.3390 (m-80) cc_final: 0.2835 (m-80) REVERT: X 15 MET cc_start: 0.5080 (tpt) cc_final: 0.4830 (tpp) REVERT: r 47 GLU cc_start: 0.5907 (tt0) cc_final: 0.5681 (tt0) REVERT: r 68 ILE cc_start: 0.6370 (mm) cc_final: 0.6081 (mm) REVERT: r 76 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 793 ASN cc_start: 0.8063 (m-40) cc_final: 0.7824 (m-40) REVERT: A 1059 SER cc_start: 0.8404 (t) cc_final: 0.8198 (p) REVERT: A 1125 ILE cc_start: 0.8792 (pt) cc_final: 0.8347 (mt) REVERT: A 1391 LEU cc_start: 0.7186 (tp) cc_final: 0.6917 (pp) REVERT: A 1486 GLU cc_start: 0.8802 (tp30) cc_final: 0.8576 (tp30) REVERT: A 1607 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7321 (tm-30) REVERT: A 1686 ASP cc_start: 0.8251 (t0) cc_final: 0.8026 (t0) REVERT: A 1734 MET cc_start: 0.7842 (ttm) cc_final: 0.7618 (ttm) outliers start: 25 outliers final: 19 residues processed: 603 average time/residue: 0.2670 time to fit residues: 260.4475 Evaluate side-chains 559 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 540 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 884 GLU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain r residue 49 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 69 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 138 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 345 optimal weight: 8.9990 chunk 95 optimal weight: 40.0000 chunk 244 optimal weight: 10.0000 chunk 322 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 chunk 298 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 385 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN I 134 ASN I 166 GLN K 379 GLN X 20 GLN A1003 HIS A1238 GLN ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 GLN A2109 ASN ** A2288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 GLN ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 133 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.172351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136468 restraints weight = 90478.078| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.33 r_work: 0.3437 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 43139 Z= 0.206 Angle : 0.603 18.533 59631 Z= 0.302 Chirality : 0.046 1.048 6896 Planarity : 0.004 0.056 7103 Dihedral : 15.321 114.534 8482 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 1.34 % Allowed : 10.63 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.44 (0.12), residues: 5104 helix: 1.30 (0.11), residues: 2288 sheet: -0.82 (0.23), residues: 490 loop : -0.40 (0.13), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 642 TYR 0.035 0.002 TYR C 831 PHE 0.028 0.002 PHE C 339 TRP 0.032 0.002 TRP C 724 HIS 0.010 0.001 HIS A1580 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (43139) covalent geometry : angle 0.60334 / 0.30 (59631) hydrogen bonds : bond 0.04602 / 2.74 ( 1940) hydrogen bonds : angle 4.89726 / 2.93 ( 5464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 558 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 358 LYS cc_start: 0.7330 (ttpt) cc_final: 0.7086 (ttpt) REVERT: I 115 ASP cc_start: 0.8009 (p0) cc_final: 0.7769 (p0) REVERT: I 146 GLU cc_start: 0.7869 (pm20) cc_final: 0.7331 (pm20) REVERT: K 334 LYS cc_start: 0.7240 (tppt) cc_final: 0.7022 (tppt) REVERT: T 993 PHE cc_start: 0.3743 (m-80) cc_final: 0.3062 (m-10) REVERT: X 15 MET cc_start: 0.5167 (tpt) cc_final: 0.4944 (tpp) REVERT: r 68 ILE cc_start: 0.6236 (mm) cc_final: 0.6010 (mm) REVERT: r 76 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 160 HIS cc_start: 0.6874 (t-90) cc_final: 0.6342 (t-90) REVERT: A 320 TYR cc_start: 0.8105 (m-80) cc_final: 0.7833 (m-80) REVERT: A 793 ASN cc_start: 0.7965 (m-40) cc_final: 0.7715 (m-40) REVERT: A 1125 ILE cc_start: 0.8774 (pt) cc_final: 0.8315 (mt) REVERT: A 1391 LEU cc_start: 0.7183 (tp) cc_final: 0.6934 (pp) REVERT: A 1486 GLU cc_start: 0.8526 (tp30) cc_final: 0.8242 (tp30) REVERT: A 1595 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: A 1607 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7162 (tm-30) outliers start: 46 outliers final: 36 residues processed: 581 average time/residue: 0.2705 time to fit residues: 253.7636 Evaluate side-chains 570 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 533 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 884 GLU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain I residue 134 ASN Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain T residue 972 THR Chi-restraints excluded: chain r residue 49 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 69 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1039 PHE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1595 GLN Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 503 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 505 optimal weight: 0.1980 chunk 124 optimal weight: 4.9990 chunk 314 optimal weight: 0.3980 chunk 242 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 446 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN I 134 ASN I 166 GLN A1238 GLN ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 GLN ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.173798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.139342 restraints weight = 89002.839| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.91 r_work: 0.3475 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 43139 Z= 0.134 Angle : 0.540 14.123 59631 Z= 0.273 Chirality : 0.041 0.456 6896 Planarity : 0.004 0.048 7103 Dihedral : 15.240 115.362 8482 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.80 % Favored : 97.18 % Rotamer: Outliers : 1.31 % Allowed : 12.15 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.52 (0.12), residues: 5104 helix: 1.39 (0.11), residues: 2295 sheet: -0.81 (0.23), residues: 492 loop : -0.38 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 159 TYR 0.018 0.001 TYR C 831 PHE 0.015 0.001 PHE A1187 TRP 0.028 0.001 TRP C 724 HIS 0.007 0.001 HIS A1580 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (43139) covalent geometry : angle 0.53978 / 0.27 (59631) hydrogen bonds : bond 0.04010 / 2.38 ( 1940) hydrogen bonds : angle 4.66285 / 2.78 ( 5464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 555 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: C 358 LYS cc_start: 0.7181 (ttpt) cc_final: 0.6932 (ttpt) REVERT: C 724 TRP cc_start: 0.5100 (m-90) cc_final: 0.4883 (m-90) REVERT: C 869 TYR cc_start: 0.8130 (m-80) cc_final: 0.7692 (m-10) REVERT: I 115 ASP cc_start: 0.8196 (p0) cc_final: 0.7964 (p0) REVERT: I 146 GLU cc_start: 0.8075 (pm20) cc_final: 0.7548 (pm20) REVERT: Q 29 MET cc_start: 0.8348 (tpp) cc_final: 0.8141 (tpp) REVERT: T 873 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7831 (mm-30) REVERT: T 931 TRP cc_start: 0.6716 (m-10) cc_final: 0.6410 (m-10) REVERT: r 68 ILE cc_start: 0.6305 (mm) cc_final: 0.6079 (mm) REVERT: r 76 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7276 (mm-30) REVERT: A 320 TYR cc_start: 0.8128 (m-80) cc_final: 0.7840 (m-80) REVERT: A 793 ASN cc_start: 0.8043 (m-40) cc_final: 0.7809 (m-40) REVERT: A 1125 ILE cc_start: 0.8861 (pt) cc_final: 0.8375 (mt) REVERT: A 1391 LEU cc_start: 0.7234 (tp) cc_final: 0.6973 (pp) REVERT: A 1486 GLU cc_start: 0.8677 (tp30) cc_final: 0.8422 (tp30) REVERT: A 1595 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7562 (mp10) outliers start: 45 outliers final: 37 residues processed: 575 average time/residue: 0.2641 time to fit residues: 244.8992 Evaluate side-chains 568 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 530 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 884 GLU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain I residue 134 ASN Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain T residue 972 THR Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 49 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 69 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 955 TRP Chi-restraints excluded: chain A residue 1039 PHE Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1595 GLN Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 32 optimal weight: 6.9990 chunk 186 optimal weight: 0.0000 chunk 388 optimal weight: 7.9990 chunk 304 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 50.0000 chunk 1 optimal weight: 10.0000 chunk 451 optimal weight: 40.0000 chunk 102 optimal weight: 0.9990 chunk 452 optimal weight: 6.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 GLN C 859 GLN I 134 ASN I 166 GLN Q 55 GLN X 20 GLN r 129 ASN A1238 GLN ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.171073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137819 restraints weight = 74638.149| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.14 r_work: 0.3419 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 43139 Z= 0.238 Angle : 0.616 10.252 59631 Z= 0.314 Chirality : 0.044 0.468 6896 Planarity : 0.005 0.048 7103 Dihedral : 15.415 114.367 8482 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.72 % Favored : 96.26 % Rotamer: Outliers : 2.04 % Allowed : 13.29 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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 (0.12), residues: 5104 helix: 1.11 (0.11), residues: 2294 sheet: -1.00 (0.23), residues: 490 loop : -0.51 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 642 TYR 0.025 0.002 TYR C 831 PHE 0.025 0.002 PHE A1187 TRP 0.021 0.002 TRP A2073 HIS 0.010 0.001 HIS A1580 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (43139) covalent geometry : angle 0.61626 / 0.31 (59631) hydrogen bonds : bond 0.04558 / 2.71 ( 1940) hydrogen bonds : angle 4.84524 / 2.88 ( 5464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 548 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: C 722 TYR cc_start: 0.3499 (OUTLIER) cc_final: 0.3244 (t80) REVERT: C 869 TYR cc_start: 0.8198 (m-80) cc_final: 0.7758 (m-10) REVERT: I 121 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6475 (mm-30) REVERT: I 129 LYS cc_start: 0.7306 (pptt) cc_final: 0.7052 (pptt) REVERT: I 146 GLU cc_start: 0.8136 (pm20) cc_final: 0.7736 (pm20) REVERT: K 391 TYR cc_start: 0.6817 (t80) cc_final: 0.6502 (t80) REVERT: T 931 TRP cc_start: 0.6980 (m-10) cc_final: 0.6512 (m100) REVERT: q 3 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: r 68 ILE cc_start: 0.6375 (mm) cc_final: 0.6140 (mm) REVERT: A 162 LYS cc_start: 0.8453 (mptt) cc_final: 0.7854 (mttm) REVERT: A 793 ASN cc_start: 0.8156 (m-40) cc_final: 0.7914 (m-40) REVERT: A 1125 ILE cc_start: 0.8794 (pt) cc_final: 0.8341 (mt) REVERT: A 1391 LEU cc_start: 0.7131 (tp) cc_final: 0.6837 (pp) REVERT: A 1486 GLU cc_start: 0.8717 (tp30) cc_final: 0.8446 (tp30) REVERT: A 1592 ASP cc_start: 0.8198 (m-30) cc_final: 0.7534 (m-30) REVERT: A 1595 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: A 2046 THR cc_start: 0.8210 (t) cc_final: 0.7951 (p) REVERT: P 185 LYS cc_start: 0.6941 (mmtp) cc_final: 0.6738 (mmtp) outliers start: 70 outliers final: 54 residues processed: 588 average time/residue: 0.2675 time to fit residues: 254.5083 Evaluate side-chains 592 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 535 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 722 TYR Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 829 GLU Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 884 GLU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain T residue 972 THR Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain q residue 3 GLU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain r residue 49 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 69 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1039 PHE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1595 GLN Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain t residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 446 optimal weight: 9.9990 chunk 389 optimal weight: 4.9990 chunk 90 optimal weight: 0.0040 chunk 459 optimal weight: 8.9990 chunk 364 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 409 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 15 optimal weight: 50.0000 chunk 502 optimal weight: 9.9990 overall best weight: 2.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN I 166 GLN A 160 HIS A 542 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 GLN ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.171963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138649 restraints weight = 81696.360| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.16 r_work: 0.3422 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 43139 Z= 0.181 Angle : 0.574 10.294 59631 Z= 0.293 Chirality : 0.042 0.441 6896 Planarity : 0.004 0.044 7103 Dihedral : 15.378 115.246 8482 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 1.99 % Allowed : 14.60 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.25 (0.12), residues: 5104 helix: 1.16 (0.11), residues: 2292 sheet: -1.02 (0.23), residues: 489 loop : -0.51 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 870 TYR 0.021 0.002 TYR I 169 PHE 0.019 0.002 PHE A1187 TRP 0.020 0.002 TRP C 724 HIS 0.008 0.001 HIS A1580 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (43139) covalent geometry : angle 0.57424 / 0.29 (59631) hydrogen bonds : bond 0.04218 / 2.50 ( 1940) hydrogen bonds : angle 4.73284 / 2.81 ( 5464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 540 time to evaluate : 1.555 Fit side-chains REVERT: C 358 LYS cc_start: 0.7114 (tttt) cc_final: 0.6831 (ttpt) REVERT: C 724 TRP cc_start: 0.5446 (m-90) cc_final: 0.4504 (m-90) REVERT: C 869 TYR cc_start: 0.7966 (m-80) cc_final: 0.7543 (m-10) REVERT: I 129 LYS cc_start: 0.7210 (pptt) cc_final: 0.6880 (pptt) REVERT: I 146 GLU cc_start: 0.7973 (pm20) cc_final: 0.7649 (pm20) REVERT: K 391 TYR cc_start: 0.6682 (t80) cc_final: 0.6371 (t80) REVERT: Q 59 TYR cc_start: 0.8453 (t80) cc_final: 0.8122 (t80) REVERT: T 873 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7348 (mm-30) REVERT: T 931 TRP cc_start: 0.6679 (m100) cc_final: 0.6085 (m100) REVERT: r 68 ILE cc_start: 0.6239 (mm) cc_final: 0.6007 (mm) REVERT: A 162 LYS cc_start: 0.8192 (mptt) cc_final: 0.7652 (mttm) REVERT: A 793 ASN cc_start: 0.7991 (m-40) cc_final: 0.7731 (m-40) REVERT: A 1125 ILE cc_start: 0.8758 (pt) cc_final: 0.8311 (mt) REVERT: A 1391 LEU cc_start: 0.7060 (tp) cc_final: 0.6763 (pp) REVERT: A 1486 GLU cc_start: 0.8500 (tp30) cc_final: 0.8215 (tp30) REVERT: A 1592 ASP cc_start: 0.7983 (m-30) cc_final: 0.7187 (m-30) REVERT: A 1595 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7390 (mp10) outliers start: 68 outliers final: 53 residues processed: 579 average time/residue: 0.2635 time to fit residues: 246.5501 Evaluate side-chains 583 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 529 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 829 GLU Chi-restraints excluded: chain C residue 884 GLU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain Q residue 26 ASP Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain T residue 972 THR Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain r residue 49 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 69 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 955 TRP Chi-restraints excluded: chain A residue 1039 PHE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1595 GLN Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain t residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 68 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 492 optimal weight: 0.9990 chunk 423 optimal weight: 0.8980 chunk 401 optimal weight: 7.9990 chunk 360 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 395 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 270 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN I 166 GLN A 181 ASN A1238 GLN ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.172220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136731 restraints weight = 85521.443| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.89 r_work: 0.3448 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 43139 Z= 0.165 Angle : 0.568 10.551 59631 Z= 0.289 Chirality : 0.042 0.440 6896 Planarity : 0.004 0.046 7103 Dihedral : 15.353 115.013 8482 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 1.72 % Allowed : 15.25 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.29 (0.12), residues: 5104 helix: 1.22 (0.11), residues: 2294 sheet: -1.05 (0.23), residues: 499 loop : -0.49 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 870 TYR 0.022 0.001 TYR I 169 PHE 0.018 0.001 PHE A1187 TRP 0.021 0.002 TRP A2073 HIS 0.008 0.001 HIS A1580 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (43139) covalent geometry : angle 0.56811 / 0.29 (59631) hydrogen bonds : bond 0.04090 / 2.43 ( 1940) hydrogen bonds : angle 4.66463 / 2.77 ( 5464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 544 time to evaluate : 1.569 Fit side-chains REVERT: C 358 LYS cc_start: 0.6995 (tttt) cc_final: 0.6651 (ttpt) REVERT: C 869 TYR cc_start: 0.8169 (m-80) cc_final: 0.7748 (m-10) REVERT: I 129 LYS cc_start: 0.7139 (pptt) cc_final: 0.6855 (pptt) REVERT: I 146 GLU cc_start: 0.8137 (pm20) cc_final: 0.7893 (pm20) REVERT: K 391 TYR cc_start: 0.6707 (t80) cc_final: 0.6391 (t80) REVERT: Q 59 TYR cc_start: 0.8507 (t80) cc_final: 0.8185 (t80) REVERT: T 910 MET cc_start: 0.7843 (tpp) cc_final: 0.7590 (tpp) REVERT: T 931 TRP cc_start: 0.6814 (m100) cc_final: 0.6149 (m100) REVERT: X 24 GLU cc_start: 0.7186 (pp20) cc_final: 0.6745 (pp20) REVERT: r 68 ILE cc_start: 0.6344 (mm) cc_final: 0.6099 (mm) REVERT: A 162 LYS cc_start: 0.8316 (mptt) cc_final: 0.7753 (mttm) REVERT: A 793 ASN cc_start: 0.8107 (m-40) cc_final: 0.7879 (m-40) REVERT: A 1125 ILE cc_start: 0.8774 (pt) cc_final: 0.8342 (mt) REVERT: A 1391 LEU cc_start: 0.7117 (tp) cc_final: 0.6809 (pp) REVERT: A 1486 GLU cc_start: 0.8689 (tp30) cc_final: 0.8412 (tp30) REVERT: A 1592 ASP cc_start: 0.8288 (m-30) cc_final: 0.7533 (m-30) REVERT: A 1595 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: A 1607 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7343 (tm-30) outliers start: 59 outliers final: 52 residues processed: 575 average time/residue: 0.2717 time to fit residues: 252.8043 Evaluate side-chains 582 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 529 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 884 GLU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain T residue 972 THR Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain r residue 49 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 69 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 955 TRP Chi-restraints excluded: chain A residue 1039 PHE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1595 GLN Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 197 ASN Chi-restraints excluded: chain t residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 450 optimal weight: 5.9990 chunk 320 optimal weight: 0.8980 chunk 170 optimal weight: 0.2980 chunk 7 optimal weight: 20.0000 chunk 460 optimal weight: 6.9990 chunk 314 optimal weight: 0.1980 chunk 519 optimal weight: 20.0000 chunk 514 optimal weight: 8.9990 chunk 196 optimal weight: 0.8980 chunk 410 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN I 166 GLN A 542 ASN A1238 GLN ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.174587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.139940 restraints weight = 89292.167| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.93 r_work: 0.3490 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 43139 Z= 0.112 Angle : 0.526 10.344 59631 Z= 0.269 Chirality : 0.040 0.360 6896 Planarity : 0.004 0.041 7103 Dihedral : 15.197 115.433 8482 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.49 % Favored : 97.49 % Rotamer: Outliers : 1.46 % Allowed : 15.95 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.56 (0.12), residues: 5104 helix: 1.46 (0.11), residues: 2289 sheet: -0.84 (0.23), residues: 494 loop : -0.39 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 870 TYR 0.024 0.001 TYR I 169 PHE 0.012 0.001 PHE P 20 TRP 0.057 0.002 TRP C 724 HIS 0.006 0.001 HIS A2309 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (43139) covalent geometry : angle 0.52622 / 0.27 (59631) hydrogen bonds : bond 0.03638 / 2.15 ( 1940) hydrogen bonds : angle 4.42968 / 2.62 ( 5464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 561 time to evaluate : 1.592 Fit side-chains REVERT: C 358 LYS cc_start: 0.6989 (tttt) cc_final: 0.6640 (ttpt) REVERT: C 520 GLU cc_start: 0.6093 (mp0) cc_final: 0.5879 (mm-30) REVERT: C 673 LYS cc_start: 0.7875 (mttt) cc_final: 0.7067 (ttpt) REVERT: C 724 TRP cc_start: 0.4354 (m-90) cc_final: 0.4086 (m-90) REVERT: C 869 TYR cc_start: 0.8120 (m-80) cc_final: 0.7787 (m-10) REVERT: I 129 LYS cc_start: 0.7160 (pptt) cc_final: 0.6773 (pptt) REVERT: Q 59 TYR cc_start: 0.8494 (t80) cc_final: 0.8164 (t80) REVERT: T 931 TRP cc_start: 0.6752 (m100) cc_final: 0.6040 (m100) REVERT: X 24 GLU cc_start: 0.7072 (pp20) cc_final: 0.6588 (pp20) REVERT: r 68 ILE cc_start: 0.6349 (mm) cc_final: 0.6103 (mm) REVERT: A 162 LYS cc_start: 0.8291 (mptt) cc_final: 0.7803 (mttm) REVERT: A 696 MET cc_start: 0.1428 (tmm) cc_final: 0.0733 (mmt) REVERT: A 793 ASN cc_start: 0.8126 (m-40) cc_final: 0.7918 (m-40) REVERT: A 1125 ILE cc_start: 0.8915 (pt) cc_final: 0.8406 (mt) REVERT: A 1391 LEU cc_start: 0.7193 (tp) cc_final: 0.6904 (pp) REVERT: A 1592 ASP cc_start: 0.8282 (m-30) cc_final: 0.7515 (m-30) REVERT: A 1595 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: A 1607 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7270 (tm-30) REVERT: S1 300 GLU cc_start: 0.7021 (tp30) cc_final: 0.6633 (tp30) REVERT: S1 303 GLU cc_start: 0.6583 (tt0) cc_final: 0.6069 (pt0) outliers start: 50 outliers final: 39 residues processed: 585 average time/residue: 0.2702 time to fit residues: 254.7984 Evaluate side-chains 573 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 533 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 829 GLU Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 884 GLU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain T residue 972 THR Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain r residue 49 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 69 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 955 TRP Chi-restraints excluded: chain A residue 1039 PHE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1595 GLN Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 197 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 22 optimal weight: 30.0000 chunk 420 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 402 optimal weight: 10.0000 chunk 406 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 313 optimal weight: 5.9990 chunk 230 optimal weight: 0.1980 chunk 244 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN K 379 GLN ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 GLN ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 133 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.173968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139323 restraints weight = 86608.558| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.94 r_work: 0.3484 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43139 Z= 0.127 Angle : 0.539 11.236 59631 Z= 0.274 Chirality : 0.041 0.369 6896 Planarity : 0.004 0.043 7103 Dihedral : 15.185 114.687 8482 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.80 % Favored : 97.18 % Rotamer: Outliers : 1.46 % Allowed : 16.00 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.59 (0.12), residues: 5104 helix: 1.49 (0.11), residues: 2288 sheet: -0.83 (0.23), residues: 491 loop : -0.37 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 870 TYR 0.024 0.001 TYR I 169 PHE 0.014 0.001 PHE A1187 TRP 0.035 0.001 TRP C 724 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (43139) covalent geometry : angle 0.53915 / 0.27 (59631) hydrogen bonds : bond 0.03712 / 2.19 ( 1940) hydrogen bonds : angle 4.41914 / 2.61 ( 5464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 541 time to evaluate : 1.515 Fit side-chains REVERT: C 358 LYS cc_start: 0.7010 (tttt) cc_final: 0.6642 (ttpt) REVERT: C 673 LYS cc_start: 0.7882 (mttt) cc_final: 0.7064 (ttpt) REVERT: C 724 TRP cc_start: 0.4399 (m-90) cc_final: 0.3873 (m-90) REVERT: C 869 TYR cc_start: 0.8130 (m-80) cc_final: 0.7776 (m-10) REVERT: I 85 ASP cc_start: 0.7710 (p0) cc_final: 0.7436 (p0) REVERT: I 129 LYS cc_start: 0.7152 (pptt) cc_final: 0.6728 (pptt) REVERT: I 146 GLU cc_start: 0.7966 (pm20) cc_final: 0.7746 (mp0) REVERT: Q 59 TYR cc_start: 0.8484 (t80) cc_final: 0.8166 (t80) REVERT: T 873 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7525 (mm-30) REVERT: T 931 TRP cc_start: 0.6878 (m100) cc_final: 0.6162 (m100) REVERT: T 973 LEU cc_start: 0.4082 (OUTLIER) cc_final: 0.2981 (mp) REVERT: X 24 GLU cc_start: 0.7073 (pp20) cc_final: 0.6569 (pp20) REVERT: q 72 TYR cc_start: 0.8672 (m-80) cc_final: 0.8471 (m-80) REVERT: r 68 ILE cc_start: 0.6318 (mm) cc_final: 0.6079 (mm) REVERT: A 162 LYS cc_start: 0.7914 (mptt) cc_final: 0.7639 (mttm) REVERT: A 696 MET cc_start: 0.1469 (tmm) cc_final: 0.0770 (mmt) REVERT: A 793 ASN cc_start: 0.8109 (m-40) cc_final: 0.7891 (m-40) REVERT: A 1067 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6194 (ppp) REVERT: A 1125 ILE cc_start: 0.8910 (pt) cc_final: 0.8404 (mt) REVERT: A 1321 GLU cc_start: 0.7797 (mp0) cc_final: 0.7571 (mp0) REVERT: A 1391 LEU cc_start: 0.7174 (tp) cc_final: 0.6890 (pp) REVERT: A 1471 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7833 (ttt180) REVERT: A 1486 GLU cc_start: 0.8650 (tp30) cc_final: 0.8406 (tp30) REVERT: A 1592 ASP cc_start: 0.8278 (m-30) cc_final: 0.7524 (m-30) REVERT: A 1595 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: A 1607 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7306 (tm-30) REVERT: S1 300 GLU cc_start: 0.6993 (tp30) cc_final: 0.6736 (tp30) REVERT: S1 303 GLU cc_start: 0.6888 (tt0) cc_final: 0.6079 (pt0) outliers start: 50 outliers final: 43 residues processed: 567 average time/residue: 0.2690 time to fit residues: 246.3772 Evaluate side-chains 573 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 526 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 829 GLU Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 884 GLU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain T residue 972 THR Chi-restraints excluded: chain T residue 973 LEU Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain r residue 49 LEU Chi-restraints excluded: chain r residue 69 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 955 TRP Chi-restraints excluded: chain A residue 1039 PHE Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1471 ARG Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1595 GLN Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 197 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 487 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 327 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 458 optimal weight: 0.0030 chunk 249 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 345 optimal weight: 0.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.174862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141991 restraints weight = 85930.068| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.56 r_work: 0.3464 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43139 Z= 0.114 Angle : 0.529 10.196 59631 Z= 0.269 Chirality : 0.040 0.355 6896 Planarity : 0.004 0.042 7103 Dihedral : 15.137 114.922 8482 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.67 % Favored : 97.32 % Rotamer: Outliers : 1.46 % Allowed : 16.09 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.65 (0.12), residues: 5104 helix: 1.53 (0.11), residues: 2289 sheet: -0.75 (0.23), residues: 496 loop : -0.36 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 870 TYR 0.025 0.001 TYR I 169 PHE 0.013 0.001 PHE A1187 TRP 0.037 0.001 TRP C 724 HIS 0.006 0.001 HIS A2309 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (43139) covalent geometry : angle 0.52920 / 0.27 (59631) hydrogen bonds : bond 0.03590 / 2.12 ( 1940) hydrogen bonds : angle 4.34903 / 2.56 ( 5464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 546 time to evaluate : 1.542 Fit side-chains REVERT: C 236 MET cc_start: 0.7868 (tpp) cc_final: 0.6738 (mpp) REVERT: C 358 LYS cc_start: 0.6947 (tttt) cc_final: 0.6598 (ttpt) REVERT: C 673 LYS cc_start: 0.7853 (mttt) cc_final: 0.7059 (ttpt) REVERT: C 724 TRP cc_start: 0.4423 (m-90) cc_final: 0.3883 (m-90) REVERT: C 869 TYR cc_start: 0.7993 (m-80) cc_final: 0.7637 (m-10) REVERT: I 85 ASP cc_start: 0.7578 (p0) cc_final: 0.7276 (p0) REVERT: I 129 LYS cc_start: 0.7016 (pptt) cc_final: 0.6515 (pptt) REVERT: Q 59 TYR cc_start: 0.8445 (t80) cc_final: 0.8109 (t80) REVERT: T 873 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7197 (mm-30) REVERT: T 901 GLN cc_start: 0.8303 (mm110) cc_final: 0.8042 (mm-40) REVERT: T 931 TRP cc_start: 0.6776 (m100) cc_final: 0.6015 (m100) REVERT: T 973 LEU cc_start: 0.4125 (OUTLIER) cc_final: 0.3262 (mp) REVERT: X 24 GLU cc_start: 0.7018 (pp20) cc_final: 0.6466 (pp20) REVERT: r 68 ILE cc_start: 0.6243 (mm) cc_final: 0.6004 (mm) REVERT: r 80 TYR cc_start: 0.7740 (m-80) cc_final: 0.7487 (m-80) REVERT: A 162 LYS cc_start: 0.7775 (mptt) cc_final: 0.7483 (mttm) REVERT: A 696 MET cc_start: 0.1430 (tmm) cc_final: 0.0753 (mmt) REVERT: A 793 ASN cc_start: 0.8029 (m-40) cc_final: 0.7809 (m-40) REVERT: A 1067 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.5838 (ppp) REVERT: A 1125 ILE cc_start: 0.8896 (pt) cc_final: 0.8384 (mt) REVERT: A 1391 LEU cc_start: 0.7138 (tp) cc_final: 0.6853 (pp) REVERT: A 1486 GLU cc_start: 0.8533 (tp30) cc_final: 0.8284 (tp30) REVERT: A 1592 ASP cc_start: 0.8065 (m-30) cc_final: 0.7284 (m-30) REVERT: A 1595 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: A 1607 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7086 (tm-30) REVERT: S1 300 GLU cc_start: 0.7044 (tp30) cc_final: 0.6802 (tp30) REVERT: S1 303 GLU cc_start: 0.6731 (tt0) cc_final: 0.5945 (pt0) outliers start: 50 outliers final: 46 residues processed: 570 average time/residue: 0.2691 time to fit residues: 249.0629 Evaluate side-chains 578 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 529 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 829 GLU Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 884 GLU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain I residue 142 MET Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain T residue 972 THR Chi-restraints excluded: chain T residue 973 LEU Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain r residue 49 LEU Chi-restraints excluded: chain r residue 69 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 955 TRP Chi-restraints excluded: chain A residue 1039 PHE Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1595 GLN Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 197 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 314 optimal weight: 6.9990 chunk 399 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 287 optimal weight: 0.0270 chunk 452 optimal weight: 10.0000 chunk 178 optimal weight: 0.4980 chunk 255 optimal weight: 10.0000 chunk 295 optimal weight: 1.9990 chunk 417 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN C 538 HIS ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 GLN C 859 GLN q 34 GLN A 160 HIS A1238 GLN ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.175685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142912 restraints weight = 80955.326| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.24 r_work: 0.3490 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 43139 Z= 0.107 Angle : 0.518 10.266 59631 Z= 0.264 Chirality : 0.040 0.335 6896 Planarity : 0.004 0.041 7103 Dihedral : 15.069 114.884 8482 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.55 % Favored : 97.43 % Rotamer: Outliers : 1.37 % Allowed : 16.36 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.72 (0.12), residues: 5104 helix: 1.58 (0.11), residues: 2293 sheet: -0.67 (0.23), residues: 498 loop : -0.32 (0.13), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 870 TYR 0.025 0.001 TYR I 169 PHE 0.014 0.001 PHE A1353 TRP 0.034 0.001 TRP C 724 HIS 0.005 0.001 HIS A2309 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (43139) covalent geometry : angle 0.51810 / 0.26 (59631) hydrogen bonds : bond 0.03499 / 2.07 ( 1940) hydrogen bonds : angle 4.27795 / 2.51 ( 5464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15833.67 seconds wall clock time: 270 minutes 7.53 seconds (16207.53 seconds total)