Starting phenix.real_space_refine on Tue Sep 15 11:47:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5fj8_3178/09_2026/5fj8_3178_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fj8_3178/09_2026/5fj8_3178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5fj8_3178/09_2026/5fj8_3178_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fj8_3178/09_2026/5fj8_3178_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5fj8_3178/09_2026/5fj8_3178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fj8_3178/09_2026/5fj8_3178.map" } resolution = 3.9 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= 0.001 sd= 0.015 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 47 5.49 5 S 207 5.16 5 C 24731 2.51 5 N 6785 2.21 5 O 7508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39284 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 11130 Classifications: {'peptide': 1422} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1355} Chain breaks: 3 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1070} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 977 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 2 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1544 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 321 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1338 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 8, 'TRANS': 155} Chain breaks: 1 Chain: "N" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain breaks: 1 Chain: "O" Number of atoms: 4329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4329 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 520} Chain breaks: 2 Chain: "P" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 738 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain breaks: 2 Chain: "Q" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 215 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "Q" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 175 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'TRANS': 34} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'UNK:plan-1': 35} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "S" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "T" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 94.000 45.198 84.507 1.00 69.62 S ATOM 510 SG CYS A 70 94.492 46.331 80.725 1.00 69.71 S ATOM 557 SG CYS A 77 94.937 48.819 83.881 1.00 53.91 S ATOM 795 SG CYS A 107 50.473 67.872 94.865 1.00 67.67 S ATOM 818 SG CYS A 110 49.395 65.494 93.282 1.00 71.41 S ATOM 1184 SG CYS A 154 47.602 69.137 94.647 1.00 70.28 S ATOM 1208 SG CYS A 157 46.713 66.703 93.045 1.00 78.54 S ATOM 19514 SG CYS B1098 79.397 55.823 74.312 1.00 61.05 S ATOM 19580 SG CYS B1107 82.799 54.047 74.634 1.00 60.21 S ATOM 19600 SG CYS B1110 80.144 52.559 72.433 1.00 64.05 S ATOM 28683 SG CYS I 5 59.974 101.770 154.476 1.00 73.16 S ATOM 28702 SG CYS I 8 62.154 98.414 154.267 1.00 71.33 S ATOM 28830 SG CYS I 26 60.614 98.910 151.043 1.00 68.41 S ATOM 29019 SG CYS J 7 152.616 89.518 105.281 1.00 43.55 S ATOM 29042 SG CYS J 10 152.752 93.559 103.704 1.00 48.76 S ATOM 29322 SG CYS J 45 152.563 94.027 106.235 1.00 55.62 S ATOM 30356 SG CYS L 31 140.661 48.770 124.424 1.00 68.36 S ATOM 30376 SG CYS L 34 139.451 50.864 127.555 1.00 73.01 S ATOM 30480 SG CYS L 48 137.280 48.157 126.175 1.00 72.01 S ATOM 30503 SG CYS L 51 140.206 47.427 127.790 1.00 76.57 S Time building chain proxies: 8.07, per 1000 atoms: 0.21 Number of scatterers: 39284 At special positions: 0 Unit cell: (189.7, 159.348, 200.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 207 16.00 P 47 15.00 O 7508 8.00 N 6785 7.00 C 24731 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: 3.67 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 67 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 8 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 26 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb=" ZN L2000 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 51 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 48 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 34 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 31 " Number of angles added : 15 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9140 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 55 sheets defined 37.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.756A pdb=" N GLN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 133 through 151 removed outlier: 3.628A pdb=" N ARG A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 removed outlier: 3.965A pdb=" N ILE A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.433A pdb=" N GLU A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 213 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.607A pdb=" N LEU A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TRP A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.395A pdb=" N MET A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 320 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.573A pdb=" N VAL A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN A 333 " --> pdb=" O ASP A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.851A pdb=" N LEU A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.759A pdb=" N GLN A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.187A pdb=" N ASN A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 456' Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.503A pdb=" N ILE A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 removed outlier: 3.516A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.609A pdb=" N GLN A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 3.555A pdb=" N PHE A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 686 removed outlier: 4.075A pdb=" N ILE A 681 " --> pdb=" O VAL A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.562A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'A' and resid 722 through 733 removed outlier: 3.552A pdb=" N LYS A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 748 removed outlier: 3.776A pdb=" N LEU A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN A 746 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 784 removed outlier: 3.528A pdb=" N VAL A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS A 781 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 857 through 860 Processing helix chain 'A' and resid 861 through 894 removed outlier: 3.504A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 875 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.842A pdb=" N ILE A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 963 through 975 removed outlier: 4.023A pdb=" N LEU A 967 " --> pdb=" O ALA A 963 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) Proline residue: A 969 - end of helix removed outlier: 4.143A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 removed outlier: 3.863A pdb=" N LYS A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1025 removed outlier: 3.507A pdb=" N ILE A1012 " --> pdb=" O LEU A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1060 removed outlier: 3.630A pdb=" N THR A1054 " --> pdb=" O ASP A1050 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1081 removed outlier: 3.547A pdb=" N LEU A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1099 removed outlier: 3.872A pdb=" N ALA A1094 " --> pdb=" O GLY A1090 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU A1099 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 3.668A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1161 removed outlier: 3.709A pdb=" N LYS A1158 " --> pdb=" O ALA A1154 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1170 Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 4.527A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1254 through 1267 removed outlier: 3.774A pdb=" N TYR A1258 " --> pdb=" O ASN A1254 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A1265 " --> pdb=" O GLN A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1306 Processing helix chain 'A' and resid 1318 through 1323 removed outlier: 3.936A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1344 Processing helix chain 'A' and resid 1351 through 1364 removed outlier: 4.261A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A1356 " --> pdb=" O PRO A1352 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A1357 " --> pdb=" O ARG A1353 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1358 " --> pdb=" O HIS A1354 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1377 removed outlier: 3.932A pdb=" N SER A1377 " --> pdb=" O ARG A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1390 removed outlier: 3.704A pdb=" N LEU A1386 " --> pdb=" O SER A1382 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1402 removed outlier: 4.291A pdb=" N LEU A1396 " --> pdb=" O THR A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1418 removed outlier: 4.000A pdb=" N ILE A1416 " --> pdb=" O SER A1412 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1428 removed outlier: 3.558A pdb=" N GLY A1426 " --> pdb=" O ILE A1423 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE A1428 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1457 removed outlier: 4.215A pdb=" N LEU A1451 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A1452 " --> pdb=" O PHE A1448 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN A1453 " --> pdb=" O GLU A1449 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A1454 " --> pdb=" O SER A1450 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A1456 " --> pdb=" O SER A1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.754A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 80 removed outlier: 3.754A pdb=" N ASP B 70 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.594A pdb=" N LYS B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 278 through 294 removed outlier: 4.353A pdb=" N ILE B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 removed outlier: 3.706A pdb=" N LEU B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 331 removed outlier: 3.608A pdb=" N ALA B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.600A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 362 " --> pdb=" O MET B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 408 removed outlier: 4.110A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 424 Processing helix chain 'B' and resid 427 through 440 Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.915A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 493 Processing helix chain 'B' and resid 529 through 536 Processing helix chain 'B' and resid 567 through 581 removed outlier: 3.612A pdb=" N PHE B 571 " --> pdb=" O PHE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 632 removed outlier: 3.733A pdb=" N ARG B 628 " --> pdb=" O ASP B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.794A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.812A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.755A pdb=" N ILE B 666 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.672A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 removed outlier: 3.805A pdb=" N LEU B 687 " --> pdb=" O VAL B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 706 removed outlier: 3.523A pdb=" N ALA B 704 " --> pdb=" O THR B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 715 through 720 removed outlier: 4.282A pdb=" N PHE B 718 " --> pdb=" O TYR B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 744 removed outlier: 3.777A pdb=" N GLU B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 743 " --> pdb=" O LYS B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 953 removed outlier: 4.749A pdb=" N SER B 951 " --> pdb=" O HIS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 952 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 971 removed outlier: 3.768A pdb=" N LEU B 961 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 993 removed outlier: 3.572A pdb=" N SER B 988 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 993 " --> pdb=" O LYS B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1073 removed outlier: 3.649A pdb=" N ASP B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1083 Processing helix chain 'B' and resid 1122 through 1133 removed outlier: 3.552A pdb=" N LYS B1126 " --> pdb=" O PRO B1122 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.519A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 removed outlier: 3.506A pdb=" N LEU C 103 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 104 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.543A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.737A pdb=" N LEU C 280 " --> pdb=" O ARG C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 288 removed outlier: 3.953A pdb=" N LYS C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 removed outlier: 3.574A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 27 removed outlier: 3.614A pdb=" N LYS D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.769A pdb=" N ASN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN D 69 " --> pdb=" O TYR D 65 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D 72 " --> pdb=" O ILE D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 removed outlier: 4.289A pdb=" N ALA D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 113 removed outlier: 3.738A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.697A pdb=" N SER D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE D 137 " --> pdb=" O HIS D 133 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 138' Processing helix chain 'D' and resid 150 through 158 removed outlier: 3.519A pdb=" N ILE D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 25 removed outlier: 3.503A pdb=" N LYS E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.729A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.814A pdb=" N PHE E 42 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 66 through 72 removed outlier: 3.622A pdb=" N PHE E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 104 removed outlier: 4.210A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 165 Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.528A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 removed outlier: 4.209A pdb=" N ILE F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.596A pdb=" N GLN G 17 " --> pdb=" O PRO G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'G' and resid 162 through 173 removed outlier: 3.727A pdb=" N LEU G 168 " --> pdb=" O LYS G 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 3.923A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 38 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.925A pdb=" N ARG J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.905A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.607A pdb=" N ALA K 116 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU K 127 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP K 129 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 140 removed outlier: 3.708A pdb=" N ALA M 136 " --> pdb=" O ASN M 132 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER M 138 " --> pdb=" O ASP M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 196 removed outlier: 3.659A pdb=" N ASP M 187 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA M 189 " --> pdb=" O TYR M 185 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU M 196 " --> pdb=" O THR M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 241 removed outlier: 3.724A pdb=" N VAL M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU M 239 " --> pdb=" O LYS M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 260 removed outlier: 4.550A pdb=" N LYS M 256 " --> pdb=" O PHE M 252 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR M 258 " --> pdb=" O GLN M 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 297 removed outlier: 3.730A pdb=" N ALA N 278 " --> pdb=" O LYS N 274 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU N 279 " --> pdb=" O GLU N 275 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA N 285 " --> pdb=" O GLU N 281 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU N 291 " --> pdb=" O HIS N 287 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET N 297 " --> pdb=" O LYS N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 369 No H-bonds generated for 'chain 'N' and resid 367 through 369' Processing helix chain 'O' and resid 46 through 57 removed outlier: 3.980A pdb=" N LYS O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 71 removed outlier: 3.631A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 84 removed outlier: 4.202A pdb=" N VAL O 80 " --> pdb=" O VAL O 76 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU O 81 " --> pdb=" O ARG O 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 101 removed outlier: 3.565A pdb=" N THR O 93 " --> pdb=" O ASP O 89 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 131 Processing helix chain 'O' and resid 133 through 143 Processing helix chain 'O' and resid 151 through 167 removed outlier: 3.944A pdb=" N ALA O 157 " --> pdb=" O LYS O 153 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER O 165 " --> pdb=" O GLN O 161 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU O 166 " --> pdb=" O ASN O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 178 removed outlier: 3.634A pdb=" N VAL O 178 " --> pdb=" O TYR O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 196 removed outlier: 3.744A pdb=" N GLU O 196 " --> pdb=" O VAL O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 208 removed outlier: 4.589A pdb=" N TYR O 208 " --> pdb=" O LYS O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 219 Processing helix chain 'O' and resid 234 through 258 removed outlier: 4.101A pdb=" N ARG O 238 " --> pdb=" O ASP O 234 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER O 239 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS O 251 " --> pdb=" O THR O 247 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE O 252 " --> pdb=" O ASP O 248 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 284 through 304 removed outlier: 3.574A pdb=" N ARG O 291 " --> pdb=" O PHE O 287 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG O 292 " --> pdb=" O MET O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 305 through 320 removed outlier: 3.833A pdb=" N ALA O 315 " --> pdb=" O VAL O 311 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU O 318 " --> pdb=" O ILE O 314 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 328 Processing helix chain 'O' and resid 341 through 361 removed outlier: 4.023A pdb=" N GLU O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL O 352 " --> pdb=" O GLU O 348 " (cutoff:3.500A) Proline residue: O 357 - end of helix removed outlier: 3.796A pdb=" N PHE O 361 " --> pdb=" O PRO O 357 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 463 removed outlier: 3.834A pdb=" N SER O 463 " --> pdb=" O ILE O 459 " (cutoff:3.500A) Processing helix chain 'O' and resid 482 through 500 removed outlier: 4.473A pdb=" N VAL O 486 " --> pdb=" O LYS O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.884A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER O 508 " --> pdb=" O ALA O 504 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG O 509 " --> pdb=" O MET O 505 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG O 512 " --> pdb=" O SER O 508 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 526 removed outlier: 3.609A pdb=" N ILE O 522 " --> pdb=" O SER O 518 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER O 524 " --> pdb=" O LYS O 520 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 541 Processing helix chain 'O' and resid 571 through 576 removed outlier: 3.736A pdb=" N PHE O 576 " --> pdb=" O HIS O 572 " (cutoff:3.500A) Processing helix chain 'O' and resid 578 through 610 removed outlier: 4.322A pdb=" N GLU O 582 " --> pdb=" O ARG O 578 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP O 583 " --> pdb=" O GLN O 579 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN O 584 " --> pdb=" O ASN O 580 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET O 585 " --> pdb=" O LEU O 581 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN O 587 " --> pdb=" O TRP O 583 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N THR O 601 " --> pdb=" O GLN O 597 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU O 602 " --> pdb=" O GLU O 598 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS O 605 " --> pdb=" O THR O 601 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 652 removed outlier: 4.181A pdb=" N LEU O 624 " --> pdb=" O LEU O 620 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN O 625 " --> pdb=" O PRO O 621 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN O 626 " --> pdb=" O SER O 622 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU O 627 " --> pdb=" O GLU O 623 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN O 631 " --> pdb=" O LEU O 627 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU O 647 " --> pdb=" O ARG O 643 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL O 650 " --> pdb=" O SER O 646 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) Processing helix chain 'P' and resid 218 through 228 removed outlier: 3.812A pdb=" N GLU P 223 " --> pdb=" O GLN P 219 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA P 228 " --> pdb=" O PHE P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 240 Processing helix chain 'P' and resid 241 through 247 removed outlier: 3.738A pdb=" N LEU P 247 " --> pdb=" O LEU P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 271 removed outlier: 3.623A pdb=" N LEU P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 68 Processing helix chain 'Q' and resid 1079 through 1086 removed outlier: 3.685A pdb=" N UNK Q1085 " --> pdb=" O UNK Q1081 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1090 through 1095 Processing sheet with id=AA, first strand: chain 'A' and resid 11 through 19 removed outlier: 5.423A pdb=" N ILE A 13 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU B1144 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLY A 15 " --> pdb=" O ARG B1142 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG B1142 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.818A pdb=" N GLY A 82 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.607A pdb=" N ALA A 112 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 179 through 180 removed outlier: 3.597A pdb=" N ASP A 220 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.533A pdb=" N LEU B1060 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.571A pdb=" N SER A 382 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 500 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 499 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 379 " --> pdb=" O MET A 517 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'A' and resid 405 through 406 removed outlier: 6.760A pdb=" N VAL A 461 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU A 433 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU A 463 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 431 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AI, first strand: chain 'A' and resid 597 through 598 removed outlier: 3.796A pdb=" N VAL H 96 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA H 28 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU H 38 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP H 41 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY H 127 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE H 112 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR H 102 " --> pdb=" O TYR H 115 " (cutoff:3.500A) Processing sheet with id=AJ, first strand: chain 'A' and resid 627 through 628 Processing sheet with id=AK, first strand: chain 'A' and resid 897 through 898 removed outlier: 7.635A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 912 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 4.321A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A1143 " --> pdb=" O LEU A1293 " (cutoff:3.500A) Processing sheet with id=AM, first strand: chain 'A' and resid 1223 through 1224 removed outlier: 3.565A pdb=" N ALA A1231 " --> pdb=" O ASN A1223 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A1186 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A1232 " --> pdb=" O ILE A1184 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A1178 " --> pdb=" O LEU A1181 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A1187 " --> pdb=" O TYR A1172 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR A1172 " --> pdb=" O ARG A1187 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A1173 " --> pdb=" O TYR I 41 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR I 41 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU I 39 " --> pdb=" O ASP A1175 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A1177 " --> pdb=" O GLY I 37 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY I 37 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'A' and resid 1429 through 1432 Processing sheet with id=BA, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.691A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET B 143 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.691A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE B 129 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 149 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'B' and resid 143 through 144 removed outlier: 3.577A pdb=" N MET B 143 " --> pdb=" O TYR B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=BC Processing sheet with id=BD, first strand: chain 'B' and resid 185 through 186 Processing sheet with id=BE, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.923A pdb=" N GLN B 197 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 196 " --> pdb=" O ARG B 472 " (cutoff:3.500A) Processing sheet with id=BF, first strand: chain 'B' and resid 206 through 209 removed outlier: 5.096A pdb=" N ILE B 215 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 234 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 217 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR B 232 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS B 243 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE B 234 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR B 241 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS B 236 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing sheet with id=BG, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=BH, first strand: chain 'B' and resid 619 through 620 Processing sheet with id=BI, first strand: chain 'B' and resid 646 through 649 removed outlier: 3.720A pdb=" N ARG B 610 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing sheet with id=BJ, first strand: chain 'B' and resid 672 through 673 removed outlier: 6.827A pdb=" N VAL B 615 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing sheet with id=BK, first strand: chain 'B' and resid 560 through 561 removed outlier: 3.977A pdb=" N ALA B 598 " --> pdb=" O ASN B 593 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 602 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER B 589 " --> pdb=" O ALA B 602 " (cutoff:3.500A) Processing sheet with id=BL, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.787A pdb=" N CYS B 785 " --> pdb=" O ARG B 904 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 904 " --> pdb=" O CYS B 785 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 882 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET B 886 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU L 56 " --> pdb=" O MET B 886 " (cutoff:3.500A) Processing sheet with id=BM, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.787A pdb=" N CYS B 785 " --> pdb=" O ARG B 904 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 904 " --> pdb=" O CYS B 785 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 882 " --> pdb=" O LEU B 899 " (cutoff:3.500A) Processing sheet with id=BN, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.828A pdb=" N THR B 977 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY B 980 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing sheet with id=BO, first strand: chain 'B' and resid 753 through 755 removed outlier: 3.647A pdb=" N GLY B 920 " --> pdb=" O PHE B 912 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 773 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE B 925 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing sheet with id=BP, first strand: chain 'B' and resid 943 through 944 removed outlier: 4.344A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=BQ, first strand: chain 'B' and resid 846 through 847 Processing sheet with id=BR, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 4.308A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET B1119 " --> pdb=" O VAL B1092 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.521A pdb=" N ARG C 293 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N LEU C 291 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N ILE C 235 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ARG C 293 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ILE C 233 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ARG C 295 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N HIS C 297 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU C 229 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE C 299 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR C 227 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.521A pdb=" N ARG C 293 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 54 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 302 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 52 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLU C 41 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 57 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ASN C 43 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 222 through 235 removed outlier: 8.584A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 11.991A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 294 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing sheet with id=CD, first strand: chain 'C' and resid 168 through 169 removed outlier: 7.574A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=CE, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.510A pdb=" N VAL C 162 " --> pdb=" O ALA C 194 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=CE Processing sheet with id=DA, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.914A pdb=" N LYS G 6 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASN G 69 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N LEU G 52 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP G 50 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ARG G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY G 43 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE G 39 " --> pdb=" O GLY G 43 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.894A pdb=" N ALA E 62 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 109 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL E 111 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE E 110 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.020A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG E 212 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=GA, first strand: chain 'G' and resid 99 through 100 Processing sheet with id=GB, first strand: chain 'G' and resid 96 through 97 Processing sheet with id=GC, first strand: chain 'G' and resid 120 through 121 removed outlier: 3.610A pdb=" N TYR G 120 " --> pdb=" O ILE G 129 " (cutoff:3.500A) Processing sheet with id=GD, first strand: chain 'G' and resid 152 through 155 removed outlier: 3.987A pdb=" N ALA G 195 " --> pdb=" O VAL G 154 " (cutoff:3.500A) Processing sheet with id=IA, first strand: chain 'I' and resid 13 through 16 removed outlier: 3.760A pdb=" N LEU I 13 " --> pdb=" O ALA I 25 " (cutoff:3.500A) Processing sheet with id=KA, first strand: chain 'K' and resid 48 through 49 Processing sheet with id=MA, first strand: chain 'M' and resid 76 through 78 Processing sheet with id=MB, first strand: chain 'M' and resid 86 through 90 removed outlier: 3.747A pdb=" N TYR M 90 " --> pdb=" O ASP N 393 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP N 393 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA N 396 " --> pdb=" O GLU N 407 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU N 407 " --> pdb=" O ALA N 396 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER N 398 " --> pdb=" O SER N 405 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER N 405 " --> pdb=" O SER N 398 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA N 400 " --> pdb=" O ALA N 403 " (cutoff:3.500A) Processing sheet with id=MC, first strand: chain 'M' and resid 121 through 123 Processing sheet with id=MD, first strand: chain 'M' and resid 152 through 153 Processing sheet with id=NA, first strand: chain 'N' and resid 364 through 365 Processing sheet with id=OA, first strand: chain 'O' and resid 74 through 75 Processing sheet with id=OB, first strand: chain 'O' and resid 201 through 202 Processing sheet with id=OC, first strand: chain 'O' and resid 471 through 472 Processing sheet with id=PA, first strand: chain 'P' and resid 254 through 256 removed outlier: 3.651A pdb=" N CYS P 260 " --> pdb=" O VAL P 256 " (cutoff:3.500A) 1221 hydrogen bonds defined for protein. 3393 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.32 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12631 1.34 - 1.46: 8776 1.46 - 1.59: 18235 1.59 - 1.72: 93 1.72 - 1.84: 336 Bond restraints: 40071 Sorted by residual: bond pdb=" CA ILE I 35 " pdb=" CB ILE I 35 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.36e-02 5.41e+03 2.04e+01 bond pdb=" CA ILE Q 43 " pdb=" CB ILE Q 43 " ideal model delta sigma weight residual 1.540 1.597 -0.057 1.36e-02 5.41e+03 1.74e+01 bond pdb=" CA THR P 236 " pdb=" CB THR P 236 " ideal model delta sigma weight residual 1.538 1.588 -0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" C3' DA S 6 " pdb=" C2' DA S 6 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" CA VAL N 378 " pdb=" CB VAL N 378 " ideal model delta sigma weight residual 1.540 1.583 -0.043 1.36e-02 5.41e+03 1.01e+01 ... (remaining 40066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 53171 3.47 - 6.95: 1040 6.95 - 10.42: 96 10.42 - 13.89: 6 13.89 - 17.37: 2 Bond angle restraints: 54315 Sorted by residual: angle pdb=" C PHE I 33 " pdb=" N PRO I 34 " pdb=" CA PRO I 34 " ideal model delta sigma weight residual 119.87 128.83 -8.96 1.04e+00 9.25e-01 7.43e+01 angle pdb=" C PRO A 858 " pdb=" N PRO A 859 " pdb=" CA PRO A 859 " ideal model delta sigma weight residual 119.84 109.58 10.26 1.25e+00 6.40e-01 6.73e+01 angle pdb=" C ASN B 856 " pdb=" N PRO B 857 " pdb=" CA PRO B 857 " ideal model delta sigma weight residual 119.90 127.19 -7.29 1.02e+00 9.61e-01 5.10e+01 angle pdb=" C LEU A 955 " pdb=" N PRO A 956 " pdb=" CA PRO A 956 " ideal model delta sigma weight residual 118.85 126.60 -7.75 1.09e+00 8.42e-01 5.06e+01 angle pdb=" CA GLU P 310 " pdb=" C GLU P 310 " pdb=" N VAL P 311 " ideal model delta sigma weight residual 119.98 113.96 6.02 8.50e-01 1.38e+00 5.02e+01 ... (remaining 54310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.14: 23650 29.14 - 58.27: 806 58.27 - 87.41: 54 87.41 - 116.54: 0 116.54 - 145.68: 2 Dihedral angle restraints: 24512 sinusoidal: 10400 harmonic: 14112 Sorted by residual: dihedral pdb=" CA LYS A 599 " pdb=" C LYS A 599 " pdb=" N PRO A 600 " pdb=" CA PRO A 600 " ideal model delta harmonic sigma weight residual -180.00 -133.59 -46.41 0 5.00e+00 4.00e-02 8.62e+01 dihedral pdb=" CA SER N 405 " pdb=" C SER N 405 " pdb=" N ALA N 406 " pdb=" CA ALA N 406 " ideal model delta harmonic sigma weight residual 180.00 141.75 38.25 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" CA ILE B 319 " pdb=" C ILE B 319 " pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta harmonic sigma weight residual -180.00 -142.38 -37.62 0 5.00e+00 4.00e-02 5.66e+01 ... (remaining 24509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4747 0.048 - 0.096: 1064 0.096 - 0.144: 309 0.144 - 0.192: 37 0.192 - 0.240: 7 Chirality restraints: 6164 Sorted by residual: chirality pdb=" CA VAL B 87 " pdb=" N VAL B 87 " pdb=" C VAL B 87 " pdb=" CB VAL B 87 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE E 127 " pdb=" N ILE E 127 " pdb=" C ILE E 127 " pdb=" CB ILE E 127 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN O 469 " pdb=" N ASN O 469 " pdb=" C ASN O 469 " pdb=" CB ASN O 469 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 6161 not shown) Planarity restraints: 6822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 599 " -0.065 5.00e-02 4.00e+02 9.83e-02 1.55e+01 pdb=" N PRO A 600 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 600 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 600 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR P 236 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO P 237 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO P 237 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO P 237 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP O 328 " -0.051 5.00e-02 4.00e+02 7.77e-02 9.66e+00 pdb=" N PRO O 329 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO O 329 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO O 329 " -0.047 5.00e-02 4.00e+02 ... (remaining 6819 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 515 2.61 - 3.18: 35258 3.18 - 3.75: 57441 3.75 - 4.33: 77182 4.33 - 4.90: 122233 Nonbonded interactions: 292629 Sorted by model distance: nonbonded pdb=" OD2 ASP A 829 " pdb=" ND2 ASN A 838 " model vdw 2.035 3.120 nonbonded pdb=" NZ LYS A 615 " pdb=" O SER A 620 " model vdw 2.049 3.120 nonbonded pdb=" OD1 ASN A 109 " pdb="ZN ZN A2001 " model vdw 2.051 2.230 nonbonded pdb=" O THR C 16 " pdb=" NH1 ARG C 295 " model vdw 2.071 3.120 nonbonded pdb=" NZ LYS B 192 " pdb=" O SER B 438 " model vdw 2.081 3.120 ... (remaining 292624 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.060 Process input model: 43.200 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 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 : 0.005 0.366 40092 Z= 0.338 Angle : 1.247 29.165 54330 Z= 0.822 Chirality : 0.045 0.240 6164 Planarity : 0.005 0.098 6822 Dihedral : 13.730 145.678 15372 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 1.14 % Allowed : 16.01 % Favored : 82.86 % Rotamer: Outliers : 4.05 % Allowed : 10.25 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.09), residues: 4742 helix: -3.69 (0.09), residues: 1422 sheet: -1.68 (0.19), residues: 535 loop : -3.27 (0.09), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 145 TYR 0.018 0.001 TYR O 223 PHE 0.041 0.001 PHE N 390 TRP 0.037 0.001 TRP D 29 HIS 0.006 0.001 HIS A1318 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.33 (40071) covalent geometry : angle 1.21345 / 0.82 (54315) hydrogen bonds : bond 0.30312 / 20.48 ( 1197) hydrogen bonds : angle 10.33037 / 7.05 ( 3393) metal coordination : bond 0.11307 / 8.68 ( 21) metal coordination : angle 17.21701 / 9.82 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1532 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1360 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.7245 (pttm) cc_final: 0.6718 (mmmt) REVERT: A 122 GLN cc_start: 0.8476 (tp-100) cc_final: 0.8271 (tp-100) REVERT: A 124 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8244 (mt) REVERT: A 147 GLN cc_start: 0.8110 (tp40) cc_final: 0.7636 (tm-30) REVERT: A 177 LYS cc_start: 0.6783 (tptm) cc_final: 0.6467 (mtpp) REVERT: A 201 TRP cc_start: 0.6604 (m100) cc_final: 0.6050 (m100) REVERT: A 517 MET cc_start: 0.8664 (mmt) cc_final: 0.8441 (mmp) REVERT: A 577 THR cc_start: 0.8294 (m) cc_final: 0.8019 (m) REVERT: A 741 LEU cc_start: 0.7984 (mt) cc_final: 0.7780 (tt) REVERT: A 870 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8012 (tm-30) REVERT: A 1003 ASP cc_start: 0.8208 (m-30) cc_final: 0.7701 (p0) REVERT: A 1028 MET cc_start: 0.3269 (mmp) cc_final: 0.1948 (mmt) REVERT: A 1357 LEU cc_start: 0.9013 (tt) cc_final: 0.8801 (tt) REVERT: A 1401 PHE cc_start: 0.7932 (t80) cc_final: 0.7723 (t80) REVERT: B 72 ASP cc_start: 0.8180 (m-30) cc_final: 0.7924 (m-30) REVERT: B 154 ILE cc_start: 0.7967 (mp) cc_final: 0.7744 (mp) REVERT: B 191 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: B 356 VAL cc_start: 0.8268 (m) cc_final: 0.7942 (p) REVERT: B 375 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7784 (mtpt) REVERT: B 545 ASP cc_start: 0.4730 (OUTLIER) cc_final: 0.4466 (t0) REVERT: B 722 ASP cc_start: 0.7917 (t0) cc_final: 0.7707 (t0) REVERT: B 723 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8758 (m) REVERT: B 774 ASN cc_start: 0.8486 (t0) cc_final: 0.8268 (t0) REVERT: B 899 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8911 (pt) REVERT: B 910 ASP cc_start: 0.8332 (m-30) cc_final: 0.7987 (m-30) REVERT: B 938 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8287 (pp) REVERT: B 1030 MET cc_start: 0.8257 (mmm) cc_final: 0.8053 (mtt) REVERT: B 1068 ASP cc_start: 0.6741 (t70) cc_final: 0.5829 (t70) REVERT: B 1103 TYR cc_start: 0.8811 (p90) cc_final: 0.8608 (p90) REVERT: C 1 MET cc_start: 0.6795 (ttt) cc_final: 0.6391 (ttt) REVERT: C 123 ASP cc_start: 0.6167 (p0) cc_final: 0.5761 (t0) REVERT: C 308 MET cc_start: 0.8170 (ptp) cc_final: 0.7655 (ptp) REVERT: D 7 ARG cc_start: 0.7089 (ttp-110) cc_final: 0.6624 (mtp-110) REVERT: D 28 LEU cc_start: 0.6411 (tt) cc_final: 0.5968 (tt) REVERT: E 46 TYR cc_start: 0.8150 (m-10) cc_final: 0.7730 (m-80) REVERT: E 61 GLN cc_start: 0.6827 (tt0) cc_final: 0.6035 (tm-30) REVERT: E 90 VAL cc_start: 0.7591 (OUTLIER) cc_final: 0.7313 (t) REVERT: E 141 VAL cc_start: 0.6732 (m) cc_final: 0.6281 (m) REVERT: E 150 VAL cc_start: 0.8389 (t) cc_final: 0.8168 (t) REVERT: F 123 LYS cc_start: 0.8552 (tptt) cc_final: 0.7960 (tttt) REVERT: G 78 LYS cc_start: 0.7320 (ttmt) cc_final: 0.6887 (pttm) REVERT: G 111 PRO cc_start: 0.7243 (Cg_endo) cc_final: 0.6662 (Cg_exo) REVERT: G 146 ILE cc_start: 0.7451 (mt) cc_final: 0.7113 (tt) REVERT: H 91 ASP cc_start: 0.6506 (m-30) cc_final: 0.6296 (m-30) REVERT: J 63 TYR cc_start: 0.8093 (m-80) cc_final: 0.7864 (m-80) REVERT: L 42 ARG cc_start: 0.6111 (tpp-160) cc_final: 0.5894 (mmp80) REVERT: N 284 ASN cc_start: 0.7483 (t0) cc_final: 0.7216 (t0) REVERT: N 297 MET cc_start: 0.7033 (mmt) cc_final: 0.6648 (ppp) REVERT: N 373 VAL cc_start: 0.7432 (OUTLIER) cc_final: 0.6997 (t) REVERT: N 374 LYS cc_start: 0.7201 (ptpt) cc_final: 0.6686 (tttp) REVERT: N 382 ILE cc_start: 0.8354 (pp) cc_final: 0.8079 (pp) REVERT: O 57 LEU cc_start: 0.7503 (mt) cc_final: 0.7298 (tp) REVERT: O 80 VAL cc_start: 0.7040 (t) cc_final: 0.6310 (p) REVERT: O 364 ILE cc_start: 0.6313 (mt) cc_final: 0.6100 (pt) REVERT: O 574 TYR cc_start: 0.6574 (m-10) cc_final: 0.6098 (m-10) REVERT: O 575 ASN cc_start: 0.6778 (t0) cc_final: 0.6137 (m-40) REVERT: O 594 LYS cc_start: 0.8430 (mmmt) cc_final: 0.7780 (mtpt) REVERT: P 183 TRP cc_start: 0.5844 (m-10) cc_final: 0.5321 (t-100) REVERT: P 267 SER cc_start: 0.6044 (t) cc_final: 0.5819 (p) REVERT: Q 56 VAL cc_start: 0.7484 (t) cc_final: 0.7271 (t) outliers start: 172 outliers final: 26 residues processed: 1478 average time/residue: 0.2410 time to fit residues: 575.9325 Evaluate side-chains 729 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 695 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1350 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 242 ASN Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 576 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 8.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 540 ASN A 566 HIS ** A 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B 334 HIS B 441 ASN B 513 ASN B 626 HIS B 655 ASN B 821 HIS ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS G 32 ASN G 201 GLN J 64 ASN N 288 GLN N 289 HIS O 161 GLN ** O 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 575 ASN P 219 GLN Q 60 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.167307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.136013 restraints weight = 70430.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134864 restraints weight = 66934.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.135787 restraints weight = 61607.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136393 restraints weight = 43457.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136435 restraints weight = 39171.642| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 40092 Z= 0.263 Angle : 1.046 42.748 54330 Z= 0.507 Chirality : 0.052 0.299 6164 Planarity : 0.007 0.107 6822 Dihedral : 12.142 145.117 5847 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.99 % Allowed : 11.91 % Favored : 87.09 % Rotamer: Outliers : 6.12 % Allowed : 17.55 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.33 % 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: -3.80 (0.10), residues: 4742 helix: -2.19 (0.11), residues: 1504 sheet: -1.48 (0.18), residues: 649 loop : -3.11 (0.10), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 534 TYR 0.028 0.003 TYR A1258 PHE 0.034 0.003 PHE G 105 TRP 0.023 0.003 TRP A 197 HIS 0.011 0.002 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.26 (40071) covalent geometry : angle 0.96123 / 0.50 (54315) hydrogen bonds : bond 0.07112 / 4.83 ( 1197) hydrogen bonds : angle 6.78963 / 4.65 ( 3393) metal coordination : bond 0.01695 / 1.06 ( 21) metal coordination : angle 24.90653 / 13.20 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 748 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.7064 (pttm) cc_final: 0.6408 (mmmt) REVERT: A 115 LEU cc_start: 0.6319 (tp) cc_final: 0.6012 (mp) REVERT: A 147 GLN cc_start: 0.8226 (tp40) cc_final: 0.7937 (tm-30) REVERT: A 376 SER cc_start: 0.9378 (p) cc_final: 0.9127 (p) REVERT: A 629 LYS cc_start: 0.7987 (tttt) cc_final: 0.7539 (tmmt) REVERT: A 712 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8571 (tt) REVERT: B 73 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8439 (mp) REVERT: B 191 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8436 (pt0) REVERT: B 192 LYS cc_start: 0.8597 (mttt) cc_final: 0.8066 (mtmt) REVERT: B 431 SER cc_start: 0.9092 (t) cc_final: 0.8770 (p) REVERT: B 723 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.8903 (m) REVERT: B 899 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9072 (pt) REVERT: B 910 ASP cc_start: 0.8722 (m-30) cc_final: 0.8471 (m-30) REVERT: B 1081 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8295 (tm-30) REVERT: C 123 ASP cc_start: 0.6514 (p0) cc_final: 0.5992 (t0) REVERT: C 308 MET cc_start: 0.8405 (ptp) cc_final: 0.8091 (ptp) REVERT: D 7 ARG cc_start: 0.7496 (ttp-110) cc_final: 0.7145 (mtp-110) REVERT: D 58 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8502 (pt) REVERT: D 107 MET cc_start: 0.3661 (ppp) cc_final: 0.3401 (ppp) REVERT: D 155 GLU cc_start: 0.6246 (pt0) cc_final: 0.5989 (tp30) REVERT: E 61 GLN cc_start: 0.6874 (tt0) cc_final: 0.6265 (tm-30) REVERT: E 87 SER cc_start: 0.8464 (t) cc_final: 0.8222 (p) REVERT: F 123 LYS cc_start: 0.8691 (tptt) cc_final: 0.8006 (tttt) REVERT: G 78 LYS cc_start: 0.7185 (ttmt) cc_final: 0.6783 (pttm) REVERT: G 111 PRO cc_start: 0.7202 (Cg_endo) cc_final: 0.6485 (Cg_exo) REVERT: G 113 ASN cc_start: 0.7009 (p0) cc_final: 0.5637 (t0) REVERT: I 32 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6377 (tm-30) REVERT: K 111 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8228 (m) REVERT: K 125 MET cc_start: 0.7620 (mmm) cc_final: 0.7203 (mmm) REVERT: L 42 ARG cc_start: 0.6425 (tpp-160) cc_final: 0.5983 (mmp80) REVERT: M 88 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6673 (t80) REVERT: M 141 ASN cc_start: 0.7389 (t0) cc_final: 0.7075 (t0) REVERT: N 288 GLN cc_start: 0.7599 (tp40) cc_final: 0.6641 (pt0) REVERT: N 295 LYS cc_start: 0.8295 (ptpt) cc_final: 0.7742 (mmtt) REVERT: N 297 MET cc_start: 0.7307 (mmt) cc_final: 0.6748 (ppp) REVERT: N 362 SER cc_start: 0.7615 (m) cc_final: 0.7398 (m) REVERT: N 374 LYS cc_start: 0.7614 (ptpt) cc_final: 0.7200 (tttp) REVERT: O 57 LEU cc_start: 0.7729 (mt) cc_final: 0.7275 (tp) REVERT: O 119 TYR cc_start: 0.7839 (m-80) cc_final: 0.7019 (m-80) REVERT: O 364 ILE cc_start: 0.7005 (mt) cc_final: 0.6721 (pt) REVERT: O 468 LEU cc_start: 0.0507 (OUTLIER) cc_final: -0.0536 (tt) REVERT: O 574 TYR cc_start: 0.7022 (m-10) cc_final: 0.6570 (m-80) REVERT: O 575 ASN cc_start: 0.7087 (t0) cc_final: 0.6057 (m-40) REVERT: O 594 LYS cc_start: 0.8369 (mmmt) cc_final: 0.7508 (mtpt) REVERT: P 180 THR cc_start: 0.4583 (OUTLIER) cc_final: 0.3891 (t) REVERT: P 183 TRP cc_start: 0.6232 (m-10) cc_final: 0.5655 (t-100) REVERT: P 267 SER cc_start: 0.6006 (t) cc_final: 0.5715 (p) outliers start: 260 outliers final: 143 residues processed: 939 average time/residue: 0.2208 time to fit residues: 347.5831 Evaluate side-chains 767 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 614 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 977 TYR Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1349 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 821 HIS Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 907 GLU Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 1006 SER Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1076 SER Chi-restraints excluded: chain B residue 1111 LYS Chi-restraints excluded: chain B residue 1145 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain M residue 88 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 161 GLN Chi-restraints excluded: chain O residue 288 MET Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 221 ILE Chi-restraints excluded: chain P residue 264 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 384 optimal weight: 0.5980 chunk 451 optimal weight: 6.9990 chunk 168 optimal weight: 0.2980 chunk 135 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 380 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 297 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 461 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 310 ASN A 477 GLN A 540 ASN ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 175 GLN C 330 ASN E 54 GLN H 133 ASN L 53 HIS N 289 HIS N 366 HIS O 154 GLN O 161 GLN O 193 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.167096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138561 restraints weight = 69930.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137477 restraints weight = 86753.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138728 restraints weight = 78719.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.138598 restraints weight = 53842.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.138949 restraints weight = 52639.416| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 40092 Z= 0.181 Angle : 0.941 40.713 54330 Z= 0.442 Chirality : 0.048 0.306 6164 Planarity : 0.006 0.101 6822 Dihedral : 11.868 145.009 5828 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.95 % Allowed : 12.08 % Favored : 86.97 % Rotamer: Outliers : 5.56 % Allowed : 19.81 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.24 % 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: -3.32 (0.11), residues: 4742 helix: -1.48 (0.12), residues: 1516 sheet: -1.28 (0.19), residues: 645 loop : -3.01 (0.11), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1079 TYR 0.031 0.002 TYR B 111 PHE 0.028 0.002 PHE G 105 TRP 0.037 0.002 TRP A 201 HIS 0.010 0.002 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (40071) covalent geometry : angle 0.84580 / 0.44 (54315) hydrogen bonds : bond 0.05646 / 3.83 ( 1197) hydrogen bonds : angle 6.10776 / 4.19 ( 3393) metal coordination : bond 0.00781 / 0.54 ( 21) metal coordination : angle 24.79624 / 13.05 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 685 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7668 (tp30) REVERT: A 49 LYS cc_start: 0.6686 (pttm) cc_final: 0.6013 (mmtt) REVERT: A 115 LEU cc_start: 0.6391 (tp) cc_final: 0.5902 (mp) REVERT: A 273 MET cc_start: 0.7033 (mmm) cc_final: 0.6788 (mmm) REVERT: A 318 TYR cc_start: 0.7206 (t80) cc_final: 0.6844 (t80) REVERT: A 376 SER cc_start: 0.9315 (p) cc_final: 0.9066 (p) REVERT: A 382 SER cc_start: 0.9068 (p) cc_final: 0.8765 (m) REVERT: A 581 SER cc_start: 0.8401 (t) cc_final: 0.7909 (p) REVERT: A 593 PRO cc_start: 0.9012 (Cg_endo) cc_final: 0.8793 (Cg_exo) REVERT: A 629 LYS cc_start: 0.7763 (tttt) cc_final: 0.7302 (tmmt) REVERT: A 669 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8092 (pp) REVERT: A 794 MET cc_start: 0.8385 (mtp) cc_final: 0.7622 (mtp) REVERT: B 143 MET cc_start: 0.4209 (ptt) cc_final: 0.3933 (ptm) REVERT: B 144 HIS cc_start: 0.6818 (OUTLIER) cc_final: 0.5834 (t-90) REVERT: B 191 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8480 (pt0) REVERT: B 396 ASN cc_start: 0.7627 (m110) cc_final: 0.7357 (m110) REVERT: B 431 SER cc_start: 0.9013 (t) cc_final: 0.8776 (p) REVERT: B 590 ILE cc_start: 0.9187 (pt) cc_final: 0.8783 (pt) REVERT: B 626 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7742 (t70) REVERT: B 703 CYS cc_start: 0.7325 (m) cc_final: 0.6833 (m) REVERT: B 723 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8912 (m) REVERT: B 910 ASP cc_start: 0.8683 (m-30) cc_final: 0.8413 (m-30) REVERT: B 1030 MET cc_start: 0.8325 (mmm) cc_final: 0.8058 (mmm) REVERT: B 1081 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8151 (tm-30) REVERT: B 1133 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8615 (tt) REVERT: C 123 ASP cc_start: 0.6307 (p0) cc_final: 0.5828 (t0) REVERT: C 308 MET cc_start: 0.8331 (ptp) cc_final: 0.8070 (ptp) REVERT: D 7 ARG cc_start: 0.7367 (ttp-110) cc_final: 0.7077 (mtp-110) REVERT: D 58 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8347 (pt) REVERT: E 46 TYR cc_start: 0.8128 (m-80) cc_final: 0.7311 (m-80) REVERT: E 61 GLN cc_start: 0.6814 (tt0) cc_final: 0.6109 (tm-30) REVERT: E 186 LEU cc_start: 0.8511 (pp) cc_final: 0.8272 (pp) REVERT: F 123 LYS cc_start: 0.8643 (tptt) cc_final: 0.7965 (tttt) REVERT: G 78 LYS cc_start: 0.7194 (ttmt) cc_final: 0.6730 (pttm) REVERT: G 111 PRO cc_start: 0.7272 (Cg_endo) cc_final: 0.6838 (Cg_exo) REVERT: G 113 ASN cc_start: 0.6929 (p0) cc_final: 0.5748 (t0) REVERT: G 119 CYS cc_start: 0.4739 (t) cc_final: 0.4410 (t) REVERT: M 88 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6939 (t80) REVERT: M 141 ASN cc_start: 0.7411 (t0) cc_final: 0.7042 (t0) REVERT: M 186 ILE cc_start: 0.5791 (OUTLIER) cc_final: 0.5112 (tp) REVERT: N 288 GLN cc_start: 0.7469 (tp40) cc_final: 0.6515 (pt0) REVERT: N 295 LYS cc_start: 0.8248 (ptpt) cc_final: 0.7766 (mmtt) REVERT: N 297 MET cc_start: 0.7588 (mmt) cc_final: 0.6818 (ppp) REVERT: N 374 LYS cc_start: 0.7667 (ptpt) cc_final: 0.7119 (tttp) REVERT: O 57 LEU cc_start: 0.7529 (mt) cc_final: 0.7228 (tp) REVERT: O 71 LEU cc_start: 0.8771 (tp) cc_final: 0.8556 (tp) REVERT: O 119 TYR cc_start: 0.7677 (m-80) cc_final: 0.6893 (m-80) REVERT: O 225 ASN cc_start: 0.5012 (m-40) cc_final: 0.4279 (t0) REVERT: O 364 ILE cc_start: 0.6593 (mt) cc_final: 0.6349 (pt) REVERT: O 468 LEU cc_start: 0.0053 (OUTLIER) cc_final: -0.0592 (tt) REVERT: O 574 TYR cc_start: 0.6945 (m-10) cc_final: 0.6536 (m-10) REVERT: O 575 ASN cc_start: 0.6895 (t0) cc_final: 0.5937 (m-40) REVERT: P 225 ILE cc_start: 0.2028 (mt) cc_final: 0.1795 (mt) REVERT: P 267 SER cc_start: 0.5755 (t) cc_final: 0.5515 (p) outliers start: 236 outliers final: 126 residues processed: 866 average time/residue: 0.2195 time to fit residues: 319.0431 Evaluate side-chains 747 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 610 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 977 TYR Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 821 HIS Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 907 GLU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1106 TRP Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1145 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 130 TRP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 63 TYR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain M residue 88 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 288 MET Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 453 ILE Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 221 ILE Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 265 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 203 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 180 optimal weight: 0.0570 chunk 224 optimal weight: 4.9990 chunk 60 optimal weight: 0.0040 chunk 389 optimal weight: 7.9990 chunk 306 optimal weight: 0.0370 chunk 430 optimal weight: 6.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 431 ASN A 618 HIS ** A 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 ASN A1058 GLN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 HIS B 754 ASN B 821 HIS B 837 GLN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS N 366 HIS ** O 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.169384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.140734 restraints weight = 69472.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139842 restraints weight = 84517.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141108 restraints weight = 75932.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140998 restraints weight = 54453.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.141541 restraints weight = 48199.318| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40092 Z= 0.146 Angle : 0.898 39.321 54330 Z= 0.414 Chirality : 0.047 0.309 6164 Planarity : 0.005 0.082 6822 Dihedral : 11.674 144.856 5822 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.99 % Allowed : 11.35 % Favored : 87.66 % Rotamer: Outliers : 5.06 % Allowed : 21.22 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 1.46 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.11), residues: 4742 helix: -1.04 (0.13), residues: 1503 sheet: -1.01 (0.20), residues: 615 loop : -2.89 (0.11), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG O 578 TYR 0.028 0.002 TYR B 111 PHE 0.029 0.002 PHE G 105 TRP 0.029 0.002 TRP O 648 HIS 0.009 0.001 HIS N 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (40071) covalent geometry : angle 0.79980 / 0.41 (54315) hydrogen bonds : bond 0.04526 / 3.07 ( 1197) hydrogen bonds : angle 5.75732 / 3.95 ( 3393) metal coordination : bond 0.00613 / 0.42 ( 21) metal coordination : angle 24.64948 / 13.07 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 688 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7626 (tp30) REVERT: A 49 LYS cc_start: 0.6606 (pttm) cc_final: 0.6275 (mmmt) REVERT: A 66 GLU cc_start: 0.6371 (tm-30) cc_final: 0.5875 (tm-30) REVERT: A 115 LEU cc_start: 0.6345 (tp) cc_final: 0.6143 (mp) REVERT: A 273 MET cc_start: 0.7055 (mmm) cc_final: 0.6796 (mmm) REVERT: A 313 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6254 (ptp) REVERT: A 318 TYR cc_start: 0.7259 (t80) cc_final: 0.6945 (t80) REVERT: A 376 SER cc_start: 0.9265 (p) cc_final: 0.8995 (p) REVERT: A 382 SER cc_start: 0.9045 (p) cc_final: 0.8787 (m) REVERT: A 581 SER cc_start: 0.8493 (t) cc_final: 0.7973 (p) REVERT: A 629 LYS cc_start: 0.7814 (tttt) cc_final: 0.7209 (tmmt) REVERT: A 794 MET cc_start: 0.8289 (mtp) cc_final: 0.7882 (mtp) REVERT: A 1202 ILE cc_start: 0.7041 (tp) cc_final: 0.6750 (tt) REVERT: A 1259 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7612 (mtt180) REVERT: B 144 HIS cc_start: 0.6804 (OUTLIER) cc_final: 0.5762 (t70) REVERT: B 230 LYS cc_start: 0.6984 (tmmt) cc_final: 0.6504 (tmmt) REVERT: B 590 ILE cc_start: 0.9191 (pt) cc_final: 0.8774 (pt) REVERT: B 703 CYS cc_start: 0.7273 (m) cc_final: 0.6756 (m) REVERT: B 723 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8867 (m) REVERT: B 910 ASP cc_start: 0.8664 (m-30) cc_final: 0.8450 (m-30) REVERT: C 14 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8191 (p0) REVERT: C 123 ASP cc_start: 0.6313 (p0) cc_final: 0.5880 (t0) REVERT: C 151 THR cc_start: 0.6420 (OUTLIER) cc_final: 0.6183 (p) REVERT: C 308 MET cc_start: 0.8295 (ptp) cc_final: 0.8045 (ptp) REVERT: D 7 ARG cc_start: 0.7332 (ttp-110) cc_final: 0.6597 (mtp-110) REVERT: D 58 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8226 (pt) REVERT: D 59 THR cc_start: 0.7803 (p) cc_final: 0.7472 (t) REVERT: E 61 GLN cc_start: 0.6332 (tt0) cc_final: 0.5957 (tm-30) REVERT: E 186 LEU cc_start: 0.8381 (pp) cc_final: 0.7903 (mt) REVERT: F 77 ASP cc_start: 0.7459 (m-30) cc_final: 0.7077 (m-30) REVERT: F 123 LYS cc_start: 0.8516 (tptt) cc_final: 0.7821 (ttpt) REVERT: G 78 LYS cc_start: 0.7012 (ttmt) cc_final: 0.6605 (pttm) REVERT: G 89 ILE cc_start: 0.3090 (OUTLIER) cc_final: 0.2847 (tt) REVERT: G 111 PRO cc_start: 0.7100 (Cg_endo) cc_final: 0.6502 (Cg_exo) REVERT: G 113 ASN cc_start: 0.6808 (p0) cc_final: 0.5510 (t0) REVERT: G 114 MET cc_start: 0.7650 (ttt) cc_final: 0.7181 (ttt) REVERT: G 119 CYS cc_start: 0.4534 (t) cc_final: 0.4094 (t) REVERT: G 209 SER cc_start: 0.7828 (t) cc_final: 0.7536 (p) REVERT: I 32 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6409 (tm-30) REVERT: J 67 GLU cc_start: 0.4783 (OUTLIER) cc_final: 0.3165 (mm-30) REVERT: K 125 MET cc_start: 0.7570 (mmm) cc_final: 0.7296 (ttp) REVERT: M 88 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6753 (t80) REVERT: M 174 GLU cc_start: 0.7047 (tt0) cc_final: 0.5978 (tp30) REVERT: N 288 GLN cc_start: 0.7349 (tp40) cc_final: 0.6492 (pt0) REVERT: N 295 LYS cc_start: 0.8078 (ptpt) cc_final: 0.7810 (mmtt) REVERT: N 297 MET cc_start: 0.7378 (mmt) cc_final: 0.6743 (ppp) REVERT: N 374 LYS cc_start: 0.7519 (ptpt) cc_final: 0.7134 (tttp) REVERT: O 129 ILE cc_start: 0.6988 (tt) cc_final: 0.6619 (mt) REVERT: O 225 ASN cc_start: 0.5076 (m-40) cc_final: 0.4416 (t0) REVERT: O 263 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6681 (mt) REVERT: O 468 LEU cc_start: 0.0101 (OUTLIER) cc_final: -0.0382 (tt) REVERT: O 499 THR cc_start: 0.5595 (m) cc_final: 0.5142 (p) REVERT: O 528 MET cc_start: 0.1524 (ttt) cc_final: 0.1093 (mtp) REVERT: O 574 TYR cc_start: 0.7018 (m-10) cc_final: 0.6785 (m-10) REVERT: O 575 ASN cc_start: 0.6831 (t0) cc_final: 0.5905 (m-40) REVERT: O 590 PHE cc_start: 0.7714 (t80) cc_final: 0.7201 (t80) REVERT: O 605 LYS cc_start: 0.6305 (mmtt) cc_final: 0.4685 (ttpt) REVERT: O 648 TRP cc_start: 0.6691 (OUTLIER) cc_final: 0.5832 (t-100) REVERT: P 267 SER cc_start: 0.5870 (t) cc_final: 0.5613 (p) outliers start: 215 outliers final: 115 residues processed: 849 average time/residue: 0.2149 time to fit residues: 307.8591 Evaluate side-chains 739 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 611 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 977 TYR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 821 HIS Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 907 GLU Chi-restraints excluded: chain B residue 916 HIS Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1145 ASP Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 TRP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 130 TRP Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 88 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 366 HIS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 369 HIS Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 476 TYR Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain P residue 221 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 164 optimal weight: 4.9990 chunk 417 optimal weight: 9.9990 chunk 379 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 260 optimal weight: 4.9990 chunk 459 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 299 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN B 754 ASN B 800 ASN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN E 5 ASN E 113 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN N 289 HIS O 56 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.160060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129690 restraints weight = 70193.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128312 restraints weight = 69090.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129879 restraints weight = 62041.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129798 restraints weight = 43118.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130118 restraints weight = 39621.334| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 40092 Z= 0.294 Angle : 1.010 42.417 54330 Z= 0.482 Chirality : 0.052 0.368 6164 Planarity : 0.007 0.089 6822 Dihedral : 11.818 145.131 5819 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 1.20 % Allowed : 13.05 % Favored : 85.74 % Rotamer: Outliers : 6.41 % Allowed : 21.65 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.15 % 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: -3.21 (0.11), residues: 4742 helix: -1.16 (0.12), residues: 1555 sheet: -1.35 (0.19), residues: 635 loop : -3.08 (0.11), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 368 TYR 0.032 0.002 TYR A 601 PHE 0.029 0.003 PHE A 91 TRP 0.033 0.003 TRP M 119 HIS 0.038 0.003 HIS N 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.29 (40071) covalent geometry : angle 0.92235 / 0.48 (54315) hydrogen bonds : bond 0.05660 / 3.85 ( 1197) hydrogen bonds : angle 5.81352 / 3.97 ( 3393) metal coordination : bond 0.01100 / 0.68 ( 21) metal coordination : angle 24.84108 / 13.11 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 615 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7801 (mp0) cc_final: 0.7515 (mp0) REVERT: A 33 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8058 (tp30) REVERT: A 49 LYS cc_start: 0.7073 (pttm) cc_final: 0.6496 (mmtt) REVERT: A 55 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8768 (t0) REVERT: A 226 LYS cc_start: 0.8389 (mmtm) cc_final: 0.7861 (pttp) REVERT: A 273 MET cc_start: 0.7189 (mmm) cc_final: 0.6939 (mmm) REVERT: A 376 SER cc_start: 0.9370 (p) cc_final: 0.9077 (p) REVERT: A 379 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8689 (p) REVERT: A 382 SER cc_start: 0.9068 (p) cc_final: 0.8699 (m) REVERT: A 581 SER cc_start: 0.8692 (t) cc_final: 0.8373 (p) REVERT: A 593 PRO cc_start: 0.9155 (Cg_endo) cc_final: 0.8945 (Cg_exo) REVERT: A 598 MET cc_start: 0.7753 (tpp) cc_final: 0.7300 (mtt) REVERT: A 629 LYS cc_start: 0.7885 (tttt) cc_final: 0.7638 (tmmt) REVERT: A 664 MET cc_start: 0.6136 (mpp) cc_final: 0.5783 (mpp) REVERT: A 669 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8311 (pp) REVERT: A 794 MET cc_start: 0.8650 (mtp) cc_final: 0.8252 (mtp) REVERT: A 823 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8533 (t) REVERT: A 1087 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8615 (p) REVERT: A 1230 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7571 (mp) REVERT: B 67 TYR cc_start: 0.7869 (t80) cc_final: 0.7601 (t80) REVERT: B 230 LYS cc_start: 0.7746 (tmmt) cc_final: 0.7341 (tmmt) REVERT: B 590 ILE cc_start: 0.9297 (pt) cc_final: 0.8878 (pt) REVERT: B 723 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9050 (m) REVERT: C 123 ASP cc_start: 0.6643 (p0) cc_final: 0.6118 (t0) REVERT: C 308 MET cc_start: 0.8296 (ptp) cc_final: 0.7868 (ptp) REVERT: D 59 THR cc_start: 0.7909 (p) cc_final: 0.7605 (t) REVERT: D 98 MET cc_start: 0.5313 (OUTLIER) cc_final: 0.4266 (tmm) REVERT: E 61 GLN cc_start: 0.6405 (tt0) cc_final: 0.5926 (tm-30) REVERT: F 77 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: F 81 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8605 (m) REVERT: F 123 LYS cc_start: 0.8715 (tptt) cc_final: 0.7980 (tttt) REVERT: G 78 LYS cc_start: 0.7265 (ttmt) cc_final: 0.6703 (pttm) REVERT: G 111 PRO cc_start: 0.7173 (Cg_endo) cc_final: 0.6473 (Cg_exo) REVERT: G 113 ASN cc_start: 0.7085 (p0) cc_final: 0.5747 (t0) REVERT: G 119 CYS cc_start: 0.5268 (t) cc_final: 0.4801 (t) REVERT: G 209 SER cc_start: 0.7835 (t) cc_final: 0.7490 (p) REVERT: K 125 MET cc_start: 0.7769 (mmm) cc_final: 0.7381 (ttp) REVERT: M 88 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6963 (t80) REVERT: M 117 HIS cc_start: 0.6398 (OUTLIER) cc_final: 0.5803 (p90) REVERT: N 288 GLN cc_start: 0.7522 (tp40) cc_final: 0.6692 (pt0) REVERT: N 295 LYS cc_start: 0.8345 (ptpt) cc_final: 0.7779 (mmtt) REVERT: N 297 MET cc_start: 0.7407 (mmt) cc_final: 0.6692 (ppp) REVERT: N 374 LYS cc_start: 0.7788 (ptpt) cc_final: 0.7400 (tttp) REVERT: O 37 LEU cc_start: 0.7516 (tp) cc_final: 0.7040 (tp) REVERT: O 39 GLN cc_start: 0.7605 (tt0) cc_final: 0.7339 (tt0) REVERT: O 238 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7152 (tpt-90) REVERT: O 284 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.5456 (pt) REVERT: O 468 LEU cc_start: 0.0664 (OUTLIER) cc_final: 0.0232 (tt) REVERT: O 486 VAL cc_start: 0.7316 (OUTLIER) cc_final: 0.7014 (p) REVERT: O 588 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7346 (tp) REVERT: O 594 LYS cc_start: 0.8312 (mmmt) cc_final: 0.7477 (mtpt) outliers start: 272 outliers final: 189 residues processed: 825 average time/residue: 0.2138 time to fit residues: 296.3967 Evaluate side-chains 781 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 575 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 977 TYR Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 371 TYR Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 821 HIS Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 907 GLU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 916 HIS Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1106 TRP Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1145 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 TRP Chi-restraints excluded: chain G residue 130 TRP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain M residue 88 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 HIS Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 223 TYR Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 284 LEU Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 364 ILE Chi-restraints excluded: chain O residue 369 HIS Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 476 TYR Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 580 ASN Chi-restraints excluded: chain O residue 581 LEU Chi-restraints excluded: chain O residue 588 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain P residue 172 ILE Chi-restraints excluded: chain P residue 221 ILE Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 265 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 290 optimal weight: 8.9990 chunk 253 optimal weight: 5.9990 chunk 323 optimal weight: 0.6980 chunk 203 optimal weight: 0.4980 chunk 387 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 365 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 ASN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 754 ASN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN G 201 GLN H 128 ASN J 64 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN N 289 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.164211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133656 restraints weight = 69985.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132449 restraints weight = 68146.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.133480 restraints weight = 58831.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133927 restraints weight = 42007.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.133987 restraints weight = 38324.907| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40092 Z= 0.151 Angle : 0.905 40.158 54330 Z= 0.419 Chirality : 0.047 0.264 6164 Planarity : 0.005 0.079 6822 Dihedral : 11.664 145.728 5818 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 1.20 % Allowed : 12.10 % Favored : 86.69 % Rotamer: Outliers : 4.92 % Allowed : 23.53 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.11), residues: 4742 helix: -0.84 (0.13), residues: 1539 sheet: -1.17 (0.20), residues: 633 loop : -2.98 (0.11), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1142 TYR 0.029 0.002 TYR A 601 PHE 0.020 0.002 PHE A 91 TRP 0.020 0.002 TRP C 31 HIS 0.014 0.001 HIS O 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (40071) covalent geometry : angle 0.80703 / 0.41 (54315) hydrogen bonds : bond 0.04490 / 3.05 ( 1197) hydrogen bonds : angle 5.50524 / 3.77 ( 3393) metal coordination : bond 0.00657 / 0.42 ( 21) metal coordination : angle 24.68568 / 13.14 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 650 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7828 (tp30) REVERT: A 49 LYS cc_start: 0.7136 (pttm) cc_final: 0.6482 (mmtt) REVERT: A 273 MET cc_start: 0.7130 (mmm) cc_final: 0.6837 (mmm) REVERT: A 376 SER cc_start: 0.9225 (p) cc_final: 0.8991 (p) REVERT: A 382 SER cc_start: 0.9088 (p) cc_final: 0.8805 (m) REVERT: A 581 SER cc_start: 0.8680 (t) cc_final: 0.8312 (p) REVERT: A 598 MET cc_start: 0.7701 (tpp) cc_final: 0.7167 (mtt) REVERT: A 629 LYS cc_start: 0.7699 (tttt) cc_final: 0.7427 (tmmt) REVERT: A 794 MET cc_start: 0.8461 (mtp) cc_final: 0.8116 (mtp) REVERT: A 1230 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7422 (mp) REVERT: B 73 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8394 (mp) REVERT: B 230 LYS cc_start: 0.7480 (tmmt) cc_final: 0.7201 (tmmt) REVERT: B 343 ARG cc_start: 0.7432 (tpt170) cc_final: 0.7203 (tpt170) REVERT: B 590 ILE cc_start: 0.9181 (pt) cc_final: 0.8797 (pt) REVERT: B 626 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.7661 (t-90) REVERT: B 703 CYS cc_start: 0.7389 (m) cc_final: 0.6963 (m) REVERT: B 723 THR cc_start: 0.9251 (t) cc_final: 0.8976 (m) REVERT: C 123 ASP cc_start: 0.6593 (p0) cc_final: 0.6037 (t0) REVERT: C 308 MET cc_start: 0.8326 (ptp) cc_final: 0.7967 (ptp) REVERT: D 59 THR cc_start: 0.7880 (p) cc_final: 0.7524 (t) REVERT: E 61 GLN cc_start: 0.6340 (tt0) cc_final: 0.5909 (tm-30) REVERT: E 186 LEU cc_start: 0.8507 (pp) cc_final: 0.8216 (mt) REVERT: F 81 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8576 (m) REVERT: F 123 LYS cc_start: 0.8625 (tptt) cc_final: 0.7908 (tttt) REVERT: G 78 LYS cc_start: 0.7213 (ttmt) cc_final: 0.6601 (pttm) REVERT: G 111 PRO cc_start: 0.7173 (Cg_endo) cc_final: 0.6645 (Cg_exo) REVERT: G 113 ASN cc_start: 0.7030 (p0) cc_final: 0.5757 (t0) REVERT: G 119 CYS cc_start: 0.5080 (t) cc_final: 0.4579 (t) REVERT: G 209 SER cc_start: 0.7819 (t) cc_final: 0.7491 (p) REVERT: H 128 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6840 (m-40) REVERT: J 48 ARG cc_start: 0.8437 (ptt90) cc_final: 0.8219 (ptm160) REVERT: M 88 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6883 (t80) REVERT: M 117 HIS cc_start: 0.6250 (OUTLIER) cc_final: 0.5832 (p90) REVERT: M 170 LEU cc_start: 0.8515 (tt) cc_final: 0.8297 (pp) REVERT: N 288 GLN cc_start: 0.7444 (tp40) cc_final: 0.6464 (pt0) REVERT: N 297 MET cc_start: 0.7534 (mmt) cc_final: 0.6586 (ppp) REVERT: N 374 LYS cc_start: 0.7750 (ptpt) cc_final: 0.7323 (tttp) REVERT: O 39 GLN cc_start: 0.7486 (tt0) cc_final: 0.7221 (tt0) REVERT: O 67 MET cc_start: 0.7389 (tmm) cc_final: 0.6945 (tpp) REVERT: O 100 GLN cc_start: 0.6509 (mm110) cc_final: 0.6177 (mt0) REVERT: O 119 TYR cc_start: 0.7729 (m-80) cc_final: 0.7435 (m-10) REVERT: O 129 ILE cc_start: 0.7224 (tt) cc_final: 0.6899 (mt) REVERT: O 225 ASN cc_start: 0.5955 (m-40) cc_final: 0.5703 (m-40) REVERT: O 238 ARG cc_start: 0.7701 (mmm-85) cc_final: 0.7206 (tpt-90) REVERT: O 468 LEU cc_start: 0.0936 (OUTLIER) cc_final: 0.0537 (tp) REVERT: O 528 MET cc_start: 0.1293 (ttt) cc_final: 0.0835 (mtp) REVERT: O 588 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7286 (tp) REVERT: O 605 LYS cc_start: 0.5995 (mmtt) cc_final: 0.4451 (ttpt) outliers start: 209 outliers final: 145 residues processed: 815 average time/residue: 0.2209 time to fit residues: 304.6927 Evaluate side-chains 743 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 588 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 977 TYR Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 821 HIS Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 907 GLU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 916 HIS Chi-restraints excluded: chain B residue 1106 TRP Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1145 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 TRP Chi-restraints excluded: chain G residue 130 TRP Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 88 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 HIS Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 366 HIS Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 223 TYR Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 369 HIS Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 476 TYR Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 588 LEU Chi-restraints excluded: chain P residue 183 TRP Chi-restraints excluded: chain P residue 221 ILE Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 265 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 364 optimal weight: 0.7980 chunk 447 optimal weight: 10.0000 chunk 25 optimal weight: 0.0070 chunk 169 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 472 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 ASN ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 ASN J 64 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS O 56 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.162014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.132689 restraints weight = 69996.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131754 restraints weight = 72074.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132750 restraints weight = 70356.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132867 restraints weight = 46682.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133140 restraints weight = 43098.421| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 40092 Z= 0.203 Angle : 0.928 41.118 54330 Z= 0.432 Chirality : 0.049 0.422 6164 Planarity : 0.006 0.072 6822 Dihedral : 11.640 146.101 5817 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 1.24 % Allowed : 13.01 % Favored : 85.74 % Rotamer: Outliers : 5.58 % Allowed : 23.58 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.11), residues: 4742 helix: -0.85 (0.13), residues: 1566 sheet: -1.28 (0.20), residues: 637 loop : -3.05 (0.11), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1142 TYR 0.028 0.002 TYR O 174 PHE 0.019 0.002 PHE O 651 TRP 0.030 0.003 TRP O 648 HIS 0.010 0.002 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (40071) covalent geometry : angle 0.83222 / 0.43 (54315) hydrogen bonds : bond 0.04686 / 3.17 ( 1197) hydrogen bonds : angle 5.46228 / 3.73 ( 3393) metal coordination : bond 0.00771 / 0.50 ( 21) metal coordination : angle 24.69914 / 13.12 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 608 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: A 49 LYS cc_start: 0.7170 (pttm) cc_final: 0.6403 (mmtt) REVERT: A 115 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5741 (mp) REVERT: A 273 MET cc_start: 0.6986 (mmm) cc_final: 0.6588 (mmm) REVERT: A 376 SER cc_start: 0.9201 (p) cc_final: 0.8949 (p) REVERT: A 382 SER cc_start: 0.9092 (p) cc_final: 0.8814 (m) REVERT: A 581 SER cc_start: 0.8649 (t) cc_final: 0.8335 (p) REVERT: A 598 MET cc_start: 0.7890 (tpp) cc_final: 0.7352 (mtt) REVERT: A 794 MET cc_start: 0.8594 (mtp) cc_final: 0.8217 (mtp) REVERT: B 67 TYR cc_start: 0.7831 (t80) cc_final: 0.7558 (t80) REVERT: B 73 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8371 (mp) REVERT: B 343 ARG cc_start: 0.7408 (tpt170) cc_final: 0.7191 (tpt170) REVERT: B 590 ILE cc_start: 0.9241 (pt) cc_final: 0.8864 (pt) REVERT: B 626 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7898 (t-90) REVERT: B 703 CYS cc_start: 0.7325 (m) cc_final: 0.6885 (m) REVERT: B 723 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.8992 (m) REVERT: B 834 MET cc_start: 0.7273 (mtp) cc_final: 0.7022 (mtp) REVERT: C 14 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8234 (p0) REVERT: C 308 MET cc_start: 0.8362 (ptp) cc_final: 0.7991 (ptp) REVERT: D 59 THR cc_start: 0.7842 (p) cc_final: 0.7500 (t) REVERT: E 61 GLN cc_start: 0.6374 (tt0) cc_final: 0.5963 (tm-30) REVERT: E 186 LEU cc_start: 0.8593 (pp) cc_final: 0.8300 (mt) REVERT: F 81 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8581 (m) REVERT: F 123 LYS cc_start: 0.8670 (tptt) cc_final: 0.7928 (tttt) REVERT: G 78 LYS cc_start: 0.7062 (ttmt) cc_final: 0.6441 (pttm) REVERT: G 89 ILE cc_start: 0.3057 (OUTLIER) cc_final: 0.2823 (tt) REVERT: G 111 PRO cc_start: 0.7188 (Cg_endo) cc_final: 0.6540 (Cg_exo) REVERT: G 113 ASN cc_start: 0.6817 (p0) cc_final: 0.5522 (t0) REVERT: G 119 CYS cc_start: 0.5255 (t) cc_final: 0.4753 (t) REVERT: G 209 SER cc_start: 0.7831 (t) cc_final: 0.7516 (p) REVERT: H 40 LEU cc_start: 0.7785 (tt) cc_final: 0.7279 (tp) REVERT: K 44 ARG cc_start: 0.5770 (ttp80) cc_final: 0.5338 (ptt180) REVERT: K 45 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6821 (mm-30) REVERT: L 38 LEU cc_start: 0.6871 (pt) cc_final: 0.6447 (mp) REVERT: M 88 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7128 (t80) REVERT: M 117 HIS cc_start: 0.6279 (OUTLIER) cc_final: 0.5833 (p90) REVERT: M 170 LEU cc_start: 0.8518 (tt) cc_final: 0.8270 (pp) REVERT: N 288 GLN cc_start: 0.7380 (tp40) cc_final: 0.6493 (pt0) REVERT: N 374 LYS cc_start: 0.7795 (ptpt) cc_final: 0.7451 (tttp) REVERT: O 39 GLN cc_start: 0.7614 (tt0) cc_final: 0.7335 (tt0) REVERT: O 67 MET cc_start: 0.7300 (tmm) cc_final: 0.6849 (tpp) REVERT: O 100 GLN cc_start: 0.6516 (mm110) cc_final: 0.6159 (mt0) REVERT: O 119 TYR cc_start: 0.7838 (m-80) cc_final: 0.7503 (m-10) REVERT: O 129 ILE cc_start: 0.7248 (tt) cc_final: 0.6902 (mt) REVERT: O 154 GLN cc_start: 0.5794 (tp40) cc_final: 0.5206 (pt0) REVERT: O 225 ASN cc_start: 0.6744 (m-40) cc_final: 0.6448 (m110) REVERT: O 238 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7171 (tpt-90) REVERT: O 297 ILE cc_start: 0.8785 (tt) cc_final: 0.8396 (mm) REVERT: O 541 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7551 (tt) REVERT: O 577 MET cc_start: 0.7328 (mmt) cc_final: 0.6772 (mmt) REVERT: O 588 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7283 (tp) REVERT: O 645 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7984 (tt) REVERT: O 648 TRP cc_start: 0.5874 (t-100) cc_final: 0.5378 (t-100) outliers start: 237 outliers final: 188 residues processed: 791 average time/residue: 0.2147 time to fit residues: 287.8767 Evaluate side-chains 785 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 584 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 977 TYR Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 821 HIS Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 907 GLU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 916 HIS Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 978 CYS Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1106 TRP Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1145 ASP Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 TRP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 130 TRP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain M residue 88 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 HIS Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 366 HIS Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 223 TYR Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 369 HIS Chi-restraints excluded: chain O residue 476 TYR Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 541 ILE Chi-restraints excluded: chain O residue 575 ASN Chi-restraints excluded: chain O residue 581 LEU Chi-restraints excluded: chain O residue 588 LEU Chi-restraints excluded: chain O residue 645 LEU Chi-restraints excluded: chain P residue 172 ILE Chi-restraints excluded: chain P residue 221 ILE Chi-restraints excluded: chain P residue 260 CYS Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 265 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 61 optimal weight: 3.9990 chunk 325 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 373 optimal weight: 4.9990 chunk 405 optimal weight: 0.4980 chunk 387 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 362 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 HIS A 477 GLN A 618 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN H 137 GLN J 53 HIS ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS O 56 HIS P 176 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.161379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131322 restraints weight = 70080.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.130786 restraints weight = 65484.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131916 restraints weight = 60533.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131723 restraints weight = 42575.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131971 restraints weight = 40451.572| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40092 Z= 0.188 Angle : 0.922 41.305 54330 Z= 0.428 Chirality : 0.048 0.316 6164 Planarity : 0.005 0.081 6822 Dihedral : 11.627 146.473 5817 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.20 % Favored : 85.58 % Rotamer: Outliers : 5.89 % Allowed : 23.70 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.11), residues: 4742 helix: -0.79 (0.13), residues: 1566 sheet: -1.30 (0.19), residues: 637 loop : -3.06 (0.11), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 303 TYR 0.027 0.002 TYR B 111 PHE 0.017 0.002 PHE B1018 TRP 0.023 0.002 TRP C 31 HIS 0.014 0.002 HIS O 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (40071) covalent geometry : angle 0.82556 / 0.42 (54315) hydrogen bonds : bond 0.04583 / 3.11 ( 1197) hydrogen bonds : angle 5.40219 / 3.69 ( 3393) metal coordination : bond 0.00743 / 0.47 ( 21) metal coordination : angle 24.68653 / 13.12 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 614 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: A 66 GLU cc_start: 0.5856 (tm-30) cc_final: 0.5530 (tm-30) REVERT: A 115 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5901 (mp) REVERT: A 273 MET cc_start: 0.7022 (mmm) cc_final: 0.6620 (mmm) REVERT: A 376 SER cc_start: 0.9169 (p) cc_final: 0.8942 (p) REVERT: A 382 SER cc_start: 0.9131 (p) cc_final: 0.8842 (m) REVERT: A 581 SER cc_start: 0.8601 (t) cc_final: 0.8241 (p) REVERT: A 598 MET cc_start: 0.7998 (tpp) cc_final: 0.7464 (mtt) REVERT: A 669 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8513 (pp) REVERT: A 681 ILE cc_start: 0.8307 (mm) cc_final: 0.8087 (mt) REVERT: A 794 MET cc_start: 0.8611 (mtp) cc_final: 0.8255 (mtp) REVERT: A 823 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8550 (t) REVERT: B 67 TYR cc_start: 0.7827 (t80) cc_final: 0.7551 (t80) REVERT: B 73 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 204 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7285 (ttm110) REVERT: B 221 THR cc_start: 0.8330 (t) cc_final: 0.8084 (p) REVERT: B 590 ILE cc_start: 0.9225 (pt) cc_final: 0.8838 (pt) REVERT: B 626 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7846 (t-90) REVERT: B 723 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.8983 (m) REVERT: B 768 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7234 (pt0) REVERT: C 308 MET cc_start: 0.8404 (ptp) cc_final: 0.8024 (ptp) REVERT: E 61 GLN cc_start: 0.6307 (tt0) cc_final: 0.5909 (tm-30) REVERT: E 99 HIS cc_start: 0.7775 (m90) cc_final: 0.7487 (m90) REVERT: E 186 LEU cc_start: 0.8597 (pp) cc_final: 0.8307 (mt) REVERT: F 81 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8592 (m) REVERT: F 123 LYS cc_start: 0.8673 (tptt) cc_final: 0.7921 (tttt) REVERT: G 78 LYS cc_start: 0.7065 (ttmt) cc_final: 0.6435 (pttm) REVERT: G 111 PRO cc_start: 0.7195 (Cg_endo) cc_final: 0.6526 (Cg_exo) REVERT: G 113 ASN cc_start: 0.6854 (p0) cc_final: 0.5533 (t0) REVERT: G 119 CYS cc_start: 0.5293 (t) cc_final: 0.4456 (t) REVERT: G 209 SER cc_start: 0.7868 (t) cc_final: 0.7552 (p) REVERT: H 40 LEU cc_start: 0.7625 (tt) cc_final: 0.7280 (tp) REVERT: I 32 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6559 (tm-30) REVERT: K 44 ARG cc_start: 0.5948 (ttp80) cc_final: 0.5377 (ptt180) REVERT: K 45 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6749 (mm-30) REVERT: L 38 LEU cc_start: 0.6892 (pt) cc_final: 0.6511 (mp) REVERT: M 88 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7140 (t80) REVERT: M 117 HIS cc_start: 0.6264 (OUTLIER) cc_final: 0.5881 (p90) REVERT: M 170 LEU cc_start: 0.8553 (tt) cc_final: 0.8260 (pp) REVERT: M 174 GLU cc_start: 0.7220 (pt0) cc_final: 0.6977 (pt0) REVERT: N 288 GLN cc_start: 0.7420 (tp40) cc_final: 0.6477 (pt0) REVERT: N 374 LYS cc_start: 0.7839 (ptpt) cc_final: 0.7426 (tttp) REVERT: O 67 MET cc_start: 0.7291 (tmm) cc_final: 0.6739 (tpp) REVERT: O 71 LEU cc_start: 0.8491 (tp) cc_final: 0.8223 (tp) REVERT: O 100 GLN cc_start: 0.6532 (mm110) cc_final: 0.6155 (mt0) REVERT: O 119 TYR cc_start: 0.7867 (m-80) cc_final: 0.7537 (m-10) REVERT: O 154 GLN cc_start: 0.5893 (tp40) cc_final: 0.5275 (pt0) REVERT: O 225 ASN cc_start: 0.6948 (m-40) cc_final: 0.6636 (m110) REVERT: O 238 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7229 (tpt-90) REVERT: O 297 ILE cc_start: 0.8797 (tt) cc_final: 0.8423 (mm) REVERT: O 484 MET cc_start: 0.6710 (mmm) cc_final: 0.6468 (mmm) REVERT: O 541 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7520 (tt) REVERT: O 577 MET cc_start: 0.7331 (mmt) cc_final: 0.6582 (mmt) REVERT: O 588 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7320 (tp) outliers start: 250 outliers final: 188 residues processed: 812 average time/residue: 0.2081 time to fit residues: 286.7529 Evaluate side-chains 789 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 587 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 977 TYR Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 821 HIS Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 907 GLU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 916 HIS Chi-restraints excluded: chain B residue 978 CYS Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1106 TRP Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1145 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 TRP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 130 TRP Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain M residue 88 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 HIS Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 366 HIS Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 223 TYR Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 369 HIS Chi-restraints excluded: chain O residue 476 TYR Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 541 ILE Chi-restraints excluded: chain O residue 588 LEU Chi-restraints excluded: chain P residue 172 ILE Chi-restraints excluded: chain P residue 221 ILE Chi-restraints excluded: chain P residue 225 ILE Chi-restraints excluded: chain P residue 260 CYS Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 265 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 220 optimal weight: 0.1980 chunk 363 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 344 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 71 optimal weight: 0.0050 chunk 319 optimal weight: 0.7980 chunk 226 optimal weight: 0.0070 chunk 341 optimal weight: 8.9990 chunk 360 optimal weight: 10.0000 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS A 815 GLN A1142 ASN A1185 GLN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN C 3 ASN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN G 69 ASN H 137 GLN J 53 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS O 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.165113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.136740 restraints weight = 69845.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135799 restraints weight = 88747.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136867 restraints weight = 72459.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137049 restraints weight = 50582.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.137124 restraints weight = 47906.623| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40092 Z= 0.144 Angle : 0.906 41.462 54330 Z= 0.415 Chirality : 0.047 0.300 6164 Planarity : 0.005 0.074 6822 Dihedral : 11.485 146.560 5817 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 1.27 % Allowed : 12.27 % Favored : 86.46 % Rotamer: Outliers : 4.05 % Allowed : 25.54 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.11), residues: 4742 helix: -0.62 (0.13), residues: 1550 sheet: -0.94 (0.20), residues: 602 loop : -2.96 (0.11), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 343 TYR 0.037 0.001 TYR O 132 PHE 0.029 0.002 PHE G 77 TRP 0.045 0.002 TRP O 648 HIS 0.036 0.001 HIS O 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (40071) covalent geometry : angle 0.80853 / 0.41 (54315) hydrogen bonds : bond 0.03907 / 2.65 ( 1197) hydrogen bonds : angle 5.26113 / 3.60 ( 3393) metal coordination : bond 0.00589 / 0.36 ( 21) metal coordination : angle 24.63996 / 13.10 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 656 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7769 (tp30) REVERT: A 66 GLU cc_start: 0.5738 (tm-30) cc_final: 0.5491 (tm-30) REVERT: A 115 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5856 (mp) REVERT: A 273 MET cc_start: 0.6974 (mmm) cc_final: 0.6509 (mmm) REVERT: A 330 ASP cc_start: 0.7437 (p0) cc_final: 0.7085 (p0) REVERT: A 376 SER cc_start: 0.9053 (p) cc_final: 0.8842 (p) REVERT: A 382 SER cc_start: 0.9018 (p) cc_final: 0.8732 (m) REVERT: A 581 SER cc_start: 0.8576 (t) cc_final: 0.8096 (p) REVERT: A 598 MET cc_start: 0.7896 (tpp) cc_final: 0.7445 (mtt) REVERT: A 681 ILE cc_start: 0.8293 (mm) cc_final: 0.8069 (mt) REVERT: A 705 LEU cc_start: 0.8691 (tp) cc_final: 0.8490 (tp) REVERT: A 794 MET cc_start: 0.8536 (mtp) cc_final: 0.8229 (mtp) REVERT: A 874 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7814 (t0) REVERT: A 1304 MET cc_start: 0.7513 (tpp) cc_final: 0.7276 (mmm) REVERT: B 67 TYR cc_start: 0.7691 (t80) cc_final: 0.7466 (t80) REVERT: B 202 LYS cc_start: 0.7269 (tptp) cc_final: 0.6775 (tmtt) REVERT: B 626 HIS cc_start: 0.8072 (OUTLIER) cc_final: 0.7681 (t-90) REVERT: B 648 TYR cc_start: 0.8321 (m-10) cc_final: 0.7776 (m-80) REVERT: B 703 CYS cc_start: 0.7163 (m) cc_final: 0.6816 (m) REVERT: B 723 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8912 (m) REVERT: C 175 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7708 (tm-30) REVERT: C 308 MET cc_start: 0.8298 (ptp) cc_final: 0.7943 (ptp) REVERT: E 118 PRO cc_start: 0.7875 (Cg_endo) cc_final: 0.7498 (Cg_exo) REVERT: E 186 LEU cc_start: 0.8433 (pp) cc_final: 0.8168 (mt) REVERT: F 81 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8547 (m) REVERT: F 123 LYS cc_start: 0.8607 (tptt) cc_final: 0.7907 (tttt) REVERT: G 78 LYS cc_start: 0.6994 (ttmt) cc_final: 0.6460 (pttm) REVERT: G 111 PRO cc_start: 0.7147 (Cg_endo) cc_final: 0.6587 (Cg_exo) REVERT: G 113 ASN cc_start: 0.6543 (p0) cc_final: 0.5268 (t0) REVERT: G 119 CYS cc_start: 0.4903 (t) cc_final: 0.4432 (t) REVERT: G 209 SER cc_start: 0.7733 (t) cc_final: 0.7435 (p) REVERT: H 40 LEU cc_start: 0.7439 (tt) cc_final: 0.7045 (tp) REVERT: K 44 ARG cc_start: 0.5783 (ttp80) cc_final: 0.5450 (ptt180) REVERT: K 45 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6793 (mm-30) REVERT: L 38 LEU cc_start: 0.6897 (pt) cc_final: 0.6443 (mp) REVERT: M 88 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.7015 (t80) REVERT: M 117 HIS cc_start: 0.5967 (OUTLIER) cc_final: 0.5718 (p90) REVERT: M 170 LEU cc_start: 0.8562 (tt) cc_final: 0.8270 (pp) REVERT: N 280 LEU cc_start: 0.7537 (pp) cc_final: 0.7231 (tp) REVERT: N 288 GLN cc_start: 0.7234 (tp40) cc_final: 0.6452 (pt0) REVERT: N 374 LYS cc_start: 0.7711 (ptpt) cc_final: 0.7409 (tttp) REVERT: O 71 LEU cc_start: 0.8333 (tp) cc_final: 0.8007 (tp) REVERT: O 119 TYR cc_start: 0.7738 (m-80) cc_final: 0.7383 (m-10) REVERT: O 129 ILE cc_start: 0.6883 (tt) cc_final: 0.6620 (mt) REVERT: O 154 GLN cc_start: 0.5839 (tp40) cc_final: 0.5265 (pt0) REVERT: O 225 ASN cc_start: 0.6957 (m-40) cc_final: 0.6693 (m110) REVERT: O 238 ARG cc_start: 0.7406 (mmm-85) cc_final: 0.6993 (tpt-90) REVERT: O 287 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5922 (t80) REVERT: O 297 ILE cc_start: 0.8676 (tt) cc_final: 0.8336 (mm) REVERT: O 528 MET cc_start: 0.1546 (ttt) cc_final: 0.1025 (mtp) REVERT: O 577 MET cc_start: 0.7157 (mmt) cc_final: 0.6467 (mmt) REVERT: O 588 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7243 (tp) REVERT: O 605 LYS cc_start: 0.5811 (mmtt) cc_final: 0.4302 (ttpt) outliers start: 172 outliers final: 132 residues processed: 786 average time/residue: 0.2087 time to fit residues: 279.1391 Evaluate side-chains 759 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 617 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 821 HIS Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 907 GLU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 916 HIS Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 1106 TRP Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1145 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 69 ASN Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 TRP Chi-restraints excluded: chain G residue 130 TRP Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 88 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 HIS Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 200 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 223 TYR Chi-restraints excluded: chain O residue 264 THR Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 476 TYR Chi-restraints excluded: chain O residue 575 ASN Chi-restraints excluded: chain O residue 588 LEU Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 260 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 401 optimal weight: 4.9990 chunk 256 optimal weight: 0.8980 chunk 266 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 375 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 331 optimal weight: 7.9990 chunk 71 optimal weight: 0.0070 chunk 306 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS A1006 HIS B 237 ASN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN C 14 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN G 69 ASN H 137 GLN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS O 56 HIS O 100 GLN ** O 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.165163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134591 restraints weight = 69865.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.133390 restraints weight = 67916.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134331 restraints weight = 59143.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134874 restraints weight = 41965.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.134923 restraints weight = 37879.184| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40092 Z= 0.146 Angle : 0.912 41.752 54330 Z= 0.417 Chirality : 0.047 0.290 6164 Planarity : 0.005 0.078 6822 Dihedral : 11.420 146.725 5817 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 1.24 % Allowed : 12.21 % Favored : 86.55 % Rotamer: Outliers : 3.72 % Allowed : 26.17 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.11), residues: 4742 helix: -0.58 (0.13), residues: 1549 sheet: -1.05 (0.20), residues: 608 loop : -2.89 (0.11), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 55 TYR 0.050 0.001 TYR O 132 PHE 0.035 0.002 PHE O 566 TRP 0.038 0.002 TRP C 31 HIS 0.012 0.001 HIS N 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (40071) covalent geometry : angle 0.81553 / 0.41 (54315) hydrogen bonds : bond 0.03880 / 2.64 ( 1197) hydrogen bonds : angle 5.21047 / 3.56 ( 3393) metal coordination : bond 0.00546 / 0.35 ( 21) metal coordination : angle 24.61375 / 13.08 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9484 Ramachandran restraints generated. 4742 Oldfield, 0 Emsley, 4742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 635 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7804 (tp30) REVERT: A 66 GLU cc_start: 0.5708 (tm-30) cc_final: 0.5447 (tm-30) REVERT: A 115 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5952 (mp) REVERT: A 273 MET cc_start: 0.6991 (mmm) cc_final: 0.6547 (mmm) REVERT: A 330 ASP cc_start: 0.7583 (p0) cc_final: 0.7232 (p0) REVERT: A 382 SER cc_start: 0.9077 (p) cc_final: 0.8801 (m) REVERT: A 581 SER cc_start: 0.8629 (t) cc_final: 0.8140 (p) REVERT: A 681 ILE cc_start: 0.8271 (mm) cc_final: 0.8032 (mt) REVERT: A 705 LEU cc_start: 0.8654 (tp) cc_final: 0.8383 (tp) REVERT: A 794 MET cc_start: 0.8625 (mtp) cc_final: 0.8260 (mtp) REVERT: A 874 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7976 (t0) REVERT: A 885 MET cc_start: 0.8273 (ttm) cc_final: 0.8070 (ttm) REVERT: B 67 TYR cc_start: 0.7728 (t80) cc_final: 0.7511 (t80) REVERT: B 202 LYS cc_start: 0.7321 (tptp) cc_final: 0.7020 (tmtt) REVERT: B 221 THR cc_start: 0.8215 (t) cc_final: 0.8011 (t) REVERT: B 626 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7757 (t-90) REVERT: B 723 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8904 (m) REVERT: C 175 GLN cc_start: 0.8424 (tp-100) cc_final: 0.7929 (tm-30) REVERT: C 308 MET cc_start: 0.8376 (ptp) cc_final: 0.8017 (ptp) REVERT: E 75 MET cc_start: 0.7250 (mmt) cc_final: 0.6786 (mmm) REVERT: E 118 PRO cc_start: 0.7747 (Cg_endo) cc_final: 0.7508 (Cg_exo) REVERT: E 186 LEU cc_start: 0.8505 (pp) cc_final: 0.8235 (mt) REVERT: F 81 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8539 (m) REVERT: F 123 LYS cc_start: 0.8618 (tptt) cc_final: 0.7879 (tttt) REVERT: G 78 LYS cc_start: 0.7097 (ttmt) cc_final: 0.6434 (pttm) REVERT: G 119 CYS cc_start: 0.5141 (t) cc_final: 0.4640 (t) REVERT: G 209 SER cc_start: 0.7828 (t) cc_final: 0.7504 (p) REVERT: K 44 ARG cc_start: 0.5834 (ttp80) cc_final: 0.5442 (ptt180) REVERT: K 45 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6843 (mm-30) REVERT: L 38 LEU cc_start: 0.7010 (pt) cc_final: 0.6443 (mp) REVERT: M 88 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6931 (t80) REVERT: M 117 HIS cc_start: 0.6094 (OUTLIER) cc_final: 0.5850 (p90) REVERT: M 170 LEU cc_start: 0.8578 (tt) cc_final: 0.8265 (pp) REVERT: N 280 LEU cc_start: 0.7531 (pp) cc_final: 0.7240 (tp) REVERT: N 288 GLN cc_start: 0.7360 (tp40) cc_final: 0.6451 (pt0) REVERT: N 374 LYS cc_start: 0.7665 (ptpt) cc_final: 0.7282 (tttp) REVERT: O 67 MET cc_start: 0.7042 (tmm) cc_final: 0.6820 (tpp) REVERT: O 129 ILE cc_start: 0.7061 (tt) cc_final: 0.6786 (mt) REVERT: O 154 GLN cc_start: 0.5810 (tp40) cc_final: 0.5134 (pt0) REVERT: O 225 ASN cc_start: 0.7116 (m-40) cc_final: 0.6867 (m110) REVERT: O 238 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.7371 (tpt-90) REVERT: O 297 ILE cc_start: 0.8552 (tt) cc_final: 0.8306 (mm) REVERT: O 528 MET cc_start: 0.1131 (ttt) cc_final: 0.0640 (mtp) REVERT: O 577 MET cc_start: 0.7166 (mmt) cc_final: 0.6517 (mmt) REVERT: O 588 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7131 (tp) REVERT: O 605 LYS cc_start: 0.5893 (mmtt) cc_final: 0.4063 (ttpt) REVERT: O 629 MET cc_start: 0.6501 (tpt) cc_final: 0.6300 (ptt) outliers start: 158 outliers final: 135 residues processed: 757 average time/residue: 0.2109 time to fit residues: 271.5303 Evaluate side-chains 753 residues out of total 4245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 609 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1395 HIS Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 ASN Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 821 HIS Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 907 GLU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 916 HIS Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 1106 TRP Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1145 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 88 TRP Chi-restraints excluded: chain G residue 130 TRP Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain M residue 88 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 HIS Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 223 TYR Chi-restraints excluded: chain O residue 264 THR Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 369 HIS Chi-restraints excluded: chain O residue 476 TYR Chi-restraints excluded: chain O residue 575 ASN Chi-restraints excluded: chain O residue 588 LEU Chi-restraints excluded: chain P residue 225 ILE Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 260 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 406 optimal weight: 8.9990 chunk 304 optimal weight: 0.9990 chunk 385 optimal weight: 0.8980 chunk 323 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 287 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 83 optimal weight: 0.0000 chunk 296 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN B 754 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN H 137 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS ** O 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 575 ASN ** 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 = 0.4036 r_free = 0.4036 target = 0.165523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.135286 restraints weight = 69994.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133650 restraints weight = 72085.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134644 restraints weight = 63102.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134958 restraints weight = 47733.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.135275 restraints weight = 41879.785| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 40092 Z= 0.210 Angle : 1.033 59.200 54330 Z= 0.520 Chirality : 0.047 0.490 6164 Planarity : 0.006 0.229 6822 Dihedral : 11.420 146.728 5817 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 1.22 % Allowed : 12.21 % Favored : 86.57 % Rotamer: Outliers : 3.77 % Allowed : 26.15 % Favored : 70.08 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.11), residues: 4742 helix: -0.58 (0.13), residues: 1549 sheet: -1.05 (0.20), residues: 595 loop : -2.90 (0.11), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1009 TYR 0.043 0.002 TYR O 132 PHE 0.040 0.002 PHE G 109 TRP 0.031 0.002 TRP C 31 HIS 0.280 0.003 HIS O 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (40071) covalent geometry : angle 0.94913 / 0.52 (54315) hydrogen bonds : bond 0.03890 / 2.65 ( 1197) hydrogen bonds : angle 5.21972 / 3.58 ( 3393) metal coordination : bond 0.00544 / 0.35 ( 21) metal coordination : angle 24.61383 / 13.08 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7339.29 seconds wall clock time: 127 minutes 32.39 seconds (7652.39 seconds total)