Starting phenix.real_space_refine on Thu Jan 16 23:56:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz0_45050/01_2025/9bz0_45050.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz0_45050/01_2025/9bz0_45050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz0_45050/01_2025/9bz0_45050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz0_45050/01_2025/9bz0_45050.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz0_45050/01_2025/9bz0_45050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz0_45050/01_2025/9bz0_45050.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 sd= 1.349 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: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 94 5.49 5 Mg 2 5.21 5 S 311 5.16 5 C 34232 2.51 5 N 9569 2.21 5 O 10469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 424 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 54687 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 11289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 11289 Classifications: {'peptide': 1425} Link IDs: {'PCIS': 1, 'PTRANS': 68, 'TRANS': 1355} Chain breaks: 3 Chain: "B" Number of atoms: 9038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9038 Classifications: {'peptide': 1129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1075} Chain breaks: 3 Chain: "C" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2089 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 15, 'TRANS': 244} Chain breaks: 1 Chain: "D" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1013 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 950 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 534 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "N" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 732 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "P" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 984 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "a" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3017 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 12, 'TRANS': 373} Chain breaks: 1 Chain: "b" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5065 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 23, 'TRANS': 597} Chain breaks: 4 Chain: "c" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1865 Classifications: {'peptide': 243} Incomplete info: {'backbone_only': 24, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 Chain: "d" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8918 Classifications: {'peptide': 1140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 1098} Chain: "e" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 429 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "f" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1817 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "C" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 87.747 55.370 171.135 1.00 40.64 S ATOM 486 SG CYS A 74 90.721 56.269 173.634 1.00 22.08 S ATOM 533 SG CYS A 81 87.187 57.537 174.135 1.00 45.03 S ATOM 768 SG CYS A 111 90.415 94.075 143.698 1.00 42.94 S ATOM 796 SG CYS A 114 94.018 93.702 143.820 1.00 23.57 S ATOM 1109 SG CYS A 154 92.537 97.023 143.764 1.00 32.83 S ATOM 1136 SG CYS A 184 92.121 95.046 140.468 1.00 41.43 S ATOM 19896 SG CYS B1119 100.914 68.528 169.202 1.00 52.10 S ATOM 19918 SG CYS B1122 97.907 70.194 167.618 1.00 48.37 S ATOM 20033 SG CYS B1137 98.572 66.720 167.188 1.00 56.78 S ATOM 21021 SG CYS C 88 63.689 39.479 234.814 1.00 49.30 S ATOM 21034 SG CYS C 90 62.940 38.489 231.235 1.00 55.58 S ATOM 21069 SG CYS C 94 60.804 37.600 234.145 1.00 39.08 S ATOM 21091 SG CYS C 97 60.917 41.291 232.763 1.00 45.60 S ATOM 28397 SG CYS I 17 28.096 124.358 149.418 1.00 27.34 S ATOM 28421 SG CYS I 20 29.164 120.804 148.881 1.00 36.66 S ATOM 28582 SG CYS I 39 31.960 123.219 148.639 1.00 35.47 S ATOM 28607 SG CYS I 42 29.222 123.406 146.152 1.00 36.29 S ATOM 28959 SG CYS I 86 18.799 128.183 192.771 1.00 53.03 S ATOM 28983 SG CYS I 89 15.186 127.275 193.542 1.00 57.20 S ATOM 29187 SG CYS I 114 17.860 124.521 193.560 1.00 48.89 S ATOM 29222 SG CYS I 119 16.589 126.321 190.373 1.00 48.33 S ATOM 29333 SG CYS J 7 45.759 68.779 230.090 1.00 31.27 S ATOM 29357 SG CYS J 10 46.727 68.346 233.710 1.00 23.40 S ATOM 29621 SG CYS J 44 45.955 71.879 232.180 1.00 33.10 S ATOM 29627 SG CYS J 45 43.316 69.291 233.121 1.00 30.29 S ATOM 30790 SG CYS L 19 34.550 43.413 195.085 1.00 44.05 S ATOM 30809 SG CYS L 22 31.691 41.281 196.460 1.00 27.27 S ATOM 30926 SG CYS L 36 33.793 39.966 193.674 1.00 39.23 S ATOM 30952 SG CYS L 39 31.480 42.879 193.049 1.00 48.96 S ATOM 31178 SG CYS M 26 52.805 94.501 131.976 1.00 55.93 S ATOM 31202 SG CYS M 29 55.417 91.908 131.040 1.00 47.74 S ATOM 31363 SG CYS M 50 56.441 95.175 132.362 1.00 42.84 S ATOM 31383 SG CYS M 53 54.912 95.351 129.006 1.00 51.99 S ATOM 42906 SG CYS c 567 60.843 158.202 171.936 1.00132.63 S ATOM 42984 SG CYS c 577 57.392 158.897 170.449 1.00132.05 S ATOM 43055 SG CYS c 585 60.188 155.198 169.779 1.00143.72 S Time building chain proxies: 22.85, per 1000 atoms: 0.42 Number of scatterers: 54687 At special positions: 0 Unit cell: (161.68, 180.48, 275.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 311 16.00 P 94 15.00 Mg 2 11.99 O 10469 8.00 N 9569 7.00 C 34232 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: 10.33 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 53 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 26 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 50 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 29 " pdb=" ZN c1001 " pdb="ZN ZN c1001 " - pdb=" ND1 HIS c 588 " pdb="ZN ZN c1001 " - pdb=" SG CYS c 567 " pdb="ZN ZN c1001 " - pdb=" SG CYS c 585 " pdb="ZN ZN c1001 " - pdb=" SG CYS c 577 " Number of angles added : 48 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12402 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 90 sheets defined 35.0% alpha, 23.0% beta 40 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 16.40 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.947A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.592A pdb=" N VAL A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.544A pdb=" N VAL A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 274 through 294 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.633A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.331A pdb=" N ARG A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.729A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.590A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.771A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.730A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.689A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.659A pdb=" N SER A 900 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 901 " --> pdb=" O GLY A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 901' Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.550A pdb=" N SER A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.561A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.515A pdb=" N GLY A1070 " --> pdb=" O ASP A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 3.961A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1144 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1180 through 1184 removed outlier: 3.968A pdb=" N THR A1184 " --> pdb=" O PRO A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1188 No H-bonds generated for 'chain 'A' and resid 1186 through 1188' Processing helix chain 'A' and resid 1189 through 1198 removed outlier: 4.478A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1207 Processing helix chain 'A' and resid 1217 through 1223 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 3.805A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A1296 " --> pdb=" O MET A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 3.588A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 removed outlier: 3.506A pdb=" N GLU A1379 " --> pdb=" O ARG A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.921A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.512A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'B' and resid 18 through 38 removed outlier: 4.534A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.592A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.525A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.797A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.549A pdb=" N ALA B 459 " --> pdb=" O GLN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 547 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 636 through 644 Processing helix chain 'B' and resid 645 through 650 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.591A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 707 through 711 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 removed outlier: 3.653A pdb=" N ASN B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 743 Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.878A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1018 removed outlier: 3.571A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.534A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.678A pdb=" N ARG D 70 " --> pdb=" O ASN D 66 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.698A pdb=" N VAL D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.714A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 136 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.606A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 133 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 47 through 51 removed outlier: 3.714A pdb=" N LYS F 50 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG F 51 " --> pdb=" O ASN F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 51' Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.065A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.861A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.049A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 Processing helix chain 'M' and resid 41 through 43 No H-bonds generated for 'chain 'M' and resid 41 through 43' Processing helix chain 'M' and resid 66 through 82 Processing helix chain 'a' and resid 2 through 10 Processing helix chain 'a' and resid 14 through 28 removed outlier: 4.349A pdb=" N LEU a 18 " --> pdb=" O ASP a 14 " (cutoff:3.500A) Processing helix chain 'a' and resid 382 through 386 Processing helix chain 'b' and resid 458 through 476 removed outlier: 4.069A pdb=" N GLN b 474 " --> pdb=" O LYS b 470 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP b 475 " --> pdb=" O LEU b 471 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS b 476 " --> pdb=" O ARG b 472 " (cutoff:3.500A) Processing helix chain 'b' and resid 500 through 505 Processing helix chain 'b' and resid 508 through 525 Processing helix chain 'b' and resid 537 through 553 removed outlier: 3.609A pdb=" N GLN b 541 " --> pdb=" O GLY b 537 " (cutoff:3.500A) Processing helix chain 'b' and resid 574 through 576 No H-bonds generated for 'chain 'b' and resid 574 through 576' Processing helix chain 'b' and resid 577 through 589 Processing helix chain 'b' and resid 606 through 617 removed outlier: 3.674A pdb=" N LEU b 610 " --> pdb=" O LYS b 606 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE b 611 " --> pdb=" O LYS b 607 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG b 612 " --> pdb=" O GLU b 608 " (cutoff:3.500A) Processing helix chain 'b' and resid 624 through 631 Processing helix chain 'b' and resid 631 through 637 Processing helix chain 'b' and resid 648 through 652 Processing helix chain 'b' and resid 656 through 663 Processing helix chain 'b' and resid 681 through 693 removed outlier: 3.944A pdb=" N LEU b 685 " --> pdb=" O ASN b 681 " (cutoff:3.500A) Processing helix chain 'b' and resid 699 through 707 Processing helix chain 'b' and resid 707 through 713 Processing helix chain 'b' and resid 720 through 739 Processing helix chain 'b' and resid 746 through 750 Processing helix chain 'b' and resid 769 through 781 Processing helix chain 'b' and resid 782 through 790 Processing helix chain 'b' and resid 795 through 808 Processing helix chain 'b' and resid 808 through 814 removed outlier: 4.018A pdb=" N PHE b 812 " --> pdb=" O HIS b 808 " (cutoff:3.500A) Processing helix chain 'b' and resid 823 through 827 Processing helix chain 'b' and resid 834 through 837 Processing helix chain 'b' and resid 838 through 855 removed outlier: 3.706A pdb=" N VAL b 843 " --> pdb=" O GLY b 839 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS b 853 " --> pdb=" O LYS b 849 " (cutoff:3.500A) Processing helix chain 'b' and resid 864 through 878 Processing helix chain 'b' and resid 890 through 904 removed outlier: 4.445A pdb=" N GLN b 895 " --> pdb=" O ILE b 891 " (cutoff:3.500A) Proline residue: b 896 - end of helix Processing helix chain 'b' and resid 937 through 946 removed outlier: 4.177A pdb=" N ASP b 941 " --> pdb=" O ASN b 937 " (cutoff:3.500A) Processing helix chain 'b' and resid 967 through 988 removed outlier: 3.684A pdb=" N LYS b 971 " --> pdb=" O THR b 967 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL b 986 " --> pdb=" O LEU b 982 " (cutoff:3.500A) Processing helix chain 'b' and resid 997 through 1002 Processing helix chain 'b' and resid 1016 through 1022 Processing helix chain 'b' and resid 1247 through 1258 Processing helix chain 'b' and resid 1268 through 1272 Processing helix chain 'b' and resid 1385 through 1398 Processing helix chain 'c' and resid 2 through 14 Processing helix chain 'c' and resid 21 through 35 Processing helix chain 'c' and resid 35 through 50 removed outlier: 3.534A pdb=" N ALA c 48 " --> pdb=" O ARG c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 70 removed outlier: 3.612A pdb=" N VAL c 70 " --> pdb=" O GLU c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 81 Processing helix chain 'c' and resid 82 through 92 Processing helix chain 'c' and resid 102 through 125 removed outlier: 3.658A pdb=" N ARG c 108 " --> pdb=" O GLU c 104 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 141 Processing helix chain 'c' and resid 604 through 618 Processing helix chain 'c' and resid 660 through 665 removed outlier: 3.781A pdb=" N GLN c 664 " --> pdb=" O LEU c 661 " (cutoff:3.500A) Processing helix chain 'c' and resid 667 through 677 removed outlier: 3.557A pdb=" N LYS c 675 " --> pdb=" O ARG c 671 " (cutoff:3.500A) Processing helix chain 'c' and resid 678 through 691 Processing helix chain 'd' and resid 381 through 384 Processing helix chain 'd' and resid 755 through 759 Processing helix chain 'd' and resid 985 through 991 Processing helix chain 'd' and resid 1044 through 1062 removed outlier: 3.710A pdb=" N LYS d1060 " --> pdb=" O ASN d1056 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL d1061 " --> pdb=" O ARG d1057 " (cutoff:3.500A) Processing helix chain 'd' and resid 1069 through 1075 Processing helix chain 'd' and resid 1091 through 1095 Processing helix chain 'd' and resid 1096 through 1100 Processing helix chain 'd' and resid 1101 through 1110 Processing helix chain 'd' and resid 1125 through 1138 removed outlier: 3.532A pdb=" N LEU d1129 " --> pdb=" O THR d1125 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 28 removed outlier: 4.168A pdb=" N SER e 28 " --> pdb=" O VAL e 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 12 Processing helix chain 'f' and resid 35 through 44 Processing helix chain 'f' and resid 48 through 53 Processing helix chain 'f' and resid 62 through 69 removed outlier: 3.612A pdb=" N LEU f 68 " --> pdb=" O GLN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 85 Processing helix chain 'f' and resid 105 through 117 Processing helix chain 'f' and resid 121 through 136 removed outlier: 4.897A pdb=" N LEU f 133 " --> pdb=" O LEU f 129 " (cutoff:3.500A) Proline residue: f 134 - end of helix Processing helix chain 'f' and resid 143 through 149 Processing helix chain 'f' and resid 153 through 163 Processing helix chain 'f' and resid 180 through 202 removed outlier: 4.126A pdb=" N PHE f 184 " --> pdb=" O GLY f 180 " (cutoff:3.500A) Processing helix chain 'f' and resid 209 through 215 Processing helix chain 'f' and resid 224 through 235 removed outlier: 3.594A pdb=" N HIS f 228 " --> pdb=" O GLY f 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.743A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.630A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.697A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.576A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.897A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.820A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.677A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB4, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB5, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB6, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.767A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 6.679A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.229A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC1, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.701A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.778A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR G 50 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.441A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AC5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.446A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 205 through 208 Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC9, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AD1, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.466A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.713A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.713A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD5, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.310A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD7, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.790A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id=AD9, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE1, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.540A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.501A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.590A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.237A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.651A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN G 91 " --> pdb=" O PHE G 98 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 118 through 120 removed outlier: 3.585A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 15 removed outlier: 5.716A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF4, first strand: chain 'M' and resid 35 through 40 Processing sheet with id=AF5, first strand: chain 'a' and resid 30 through 32 Processing sheet with id=AF6, first strand: chain 'a' and resid 36 through 38 removed outlier: 7.140A pdb=" N ASP a 37 " --> pdb=" O CYS a 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'a' and resid 46 through 51 removed outlier: 6.319A pdb=" N ASP a 72 " --> pdb=" O ALA a 86 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ALA a 86 " --> pdb=" O ASP a 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 102 through 107 removed outlier: 3.656A pdb=" N THR a 104 " --> pdb=" O SER a 118 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU a 124 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL a 137 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL a 126 " --> pdb=" O ALA a 135 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 144 through 149 removed outlier: 4.164A pdb=" N HIS a 180 " --> pdb=" O LEU a 170 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 189 through 194 removed outlier: 3.542A pdb=" N ALA a 191 " --> pdb=" O ALA a 205 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE a 224 " --> pdb=" O LEU a 213 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 248 through 253 removed outlier: 3.802A pdb=" N ARG a 268 " --> pdb=" O GLY a 264 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 298 through 299 removed outlier: 6.118A pdb=" N ILE a 316 " --> pdb=" O MET a 329 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET a 329 " --> pdb=" O ILE a 316 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL a 318 " --> pdb=" O ILE a 327 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 491 through 492 Processing sheet with id=AG5, first strand: chain 'b' and resid 594 through 597 removed outlier: 6.413A pdb=" N THR b 569 " --> pdb=" O LEU b 621 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR b 623 " --> pdb=" O THR b 569 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE b 571 " --> pdb=" O THR b 623 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE b 529 " --> pdb=" O LEU b 743 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b' and resid 882 through 885 removed outlier: 6.437A pdb=" N LEU b 883 " --> pdb=" O LEU b 911 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR b 913 " --> pdb=" O LEU b 883 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N MET b 885 " --> pdb=" O THR b 913 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL b 929 " --> pdb=" O TYR b 960 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU b 962 " --> pdb=" O VAL b 929 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE b 931 " --> pdb=" O LEU b 962 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N THR b 964 " --> pdb=" O ILE b 931 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN b 760 " --> pdb=" O VAL b 959 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ARG b 961 " --> pdb=" O ASN b 760 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN b 762 " --> pdb=" O ARG b 961 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU b 963 " --> pdb=" O GLN b 762 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU b 764 " --> pdb=" O LEU b 963 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLU b 761 " --> pdb=" O LYS b1267 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LYS b1267 " --> pdb=" O GLU b 761 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL b 763 " --> pdb=" O VAL b1265 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL b1265 " --> pdb=" O VAL b 763 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE b 765 " --> pdb=" O HIS b1263 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 584 through 585 Processing sheet with id=AG8, first strand: chain 'd' and resid 1004 through 1009 removed outlier: 5.535A pdb=" N GLY d1026 " --> pdb=" O SER d1042 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER d1042 " --> pdb=" O GLY d1026 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE d1037 " --> pdb=" O ALA d 9 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'd' and resid 15 through 21 removed outlier: 3.636A pdb=" N LYS d 35 " --> pdb=" O ARG d 38 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL d 43 " --> pdb=" O PRO d 51 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR d 45 " --> pdb=" O LEU d 49 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU d 49 " --> pdb=" O THR d 45 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'd' and resid 61 through 67 removed outlier: 3.924A pdb=" N ASN d 85 " --> pdb=" O THR d 81 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA d 86 " --> pdb=" O HIS d 105 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N HIS d 105 " --> pdb=" O ALA d 86 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE d 88 " --> pdb=" O ARG d 103 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'd' and resid 121 through 124 removed outlier: 4.190A pdb=" N LYS d 153 " --> pdb=" O PRO d 144 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 163 through 169 removed outlier: 5.837A pdb=" N VAL d 164 " --> pdb=" O GLN d 183 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN d 183 " --> pdb=" O VAL d 164 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP d 166 " --> pdb=" O VAL d 181 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU d 201 " --> pdb=" O SER d 196 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'd' and resid 163 through 169 removed outlier: 5.837A pdb=" N VAL d 164 " --> pdb=" O GLN d 183 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN d 183 " --> pdb=" O VAL d 164 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP d 166 " --> pdb=" O VAL d 181 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 218 through 221 Processing sheet with id=AH6, first strand: chain 'd' and resid 258 through 263 removed outlier: 4.357A pdb=" N ARG d 279 " --> pdb=" O ASP d 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY d 306 " --> pdb=" O LEU d 280 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET d 282 " --> pdb=" O LEU d 304 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU d 304 " --> pdb=" O MET d 282 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 286 through 289 removed outlier: 6.710A pdb=" N GLU d 286 " --> pdb=" O LYS d 298 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 313 through 316 removed outlier: 6.699A pdb=" N SER d 331 " --> pdb=" O THR d 352 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR d 352 " --> pdb=" O SER d 331 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU d 333 " --> pdb=" O MET d 350 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'd' and resid 359 through 365 removed outlier: 3.879A pdb=" N ASP d 361 " --> pdb=" O CYS d 378 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'd' and resid 396 through 403 removed outlier: 6.581A pdb=" N ILE d 701 " --> pdb=" O HIS d 399 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER d 401 " --> pdb=" O LEU d 699 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU d 699 " --> pdb=" O SER d 401 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'd' and resid 409 through 413 removed outlier: 3.699A pdb=" N GLY d 409 " --> pdb=" O SER d 428 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'd' and resid 457 through 463 removed outlier: 6.791A pdb=" N VAL d 476 " --> pdb=" O GLU d 489 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU d 489 " --> pdb=" O VAL d 476 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU d 478 " --> pdb=" O VAL d 487 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'd' and resid 500 through 503 removed outlier: 3.585A pdb=" N SER d 530 " --> pdb=" O TYR d 518 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN d 520 " --> pdb=" O GLN d 528 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLN d 528 " --> pdb=" O GLN d 520 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N HIS d 522 " --> pdb=" O LEU d 526 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU d 526 " --> pdb=" O HIS d 522 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'd' and resid 538 through 542 removed outlier: 6.359A pdb=" N GLY d 559 " --> pdb=" O ALA d 539 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU d 541 " --> pdb=" O ALA d 557 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA d 557 " --> pdb=" O LEU d 541 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER d 565 " --> pdb=" O LEU d 560 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS d 570 " --> pdb=" O LEU d 576 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU d 576 " --> pdb=" O LYS d 570 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'd' and resid 588 through 596 removed outlier: 4.947A pdb=" N HIS d 600 " --> pdb=" O LEU d 616 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA d 610 " --> pdb=" O LEU d 606 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLY d 615 " --> pdb=" O ASP d 625 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASP d 625 " --> pdb=" O GLY d 615 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'd' and resid 637 through 643 removed outlier: 8.823A pdb=" N THR d 647 " --> pdb=" O SER d 661 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N SER d 661 " --> pdb=" O THR d 647 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'd' and resid 720 through 727 removed outlier: 6.417A pdb=" N LEU d 736 " --> pdb=" O ARG d 722 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE d 724 " --> pdb=" O GLY d 734 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY d 734 " --> pdb=" O ILE d 724 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR d 726 " --> pdb=" O CYS d 732 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS d 732 " --> pdb=" O TYR d 726 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'd' and resid 720 through 727 removed outlier: 6.417A pdb=" N LEU d 736 " --> pdb=" O ARG d 722 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE d 724 " --> pdb=" O GLY d 734 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY d 734 " --> pdb=" O ILE d 724 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR d 726 " --> pdb=" O CYS d 732 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS d 732 " --> pdb=" O TYR d 726 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS d 803 " --> pdb=" O ILE d 793 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP d 795 " --> pdb=" O VAL d 801 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL d 801 " --> pdb=" O ASP d 795 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER d 762 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLN d 806 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER d 764 " --> pdb=" O GLN d 806 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'd' and resid 811 through 819 removed outlier: 6.541A pdb=" N GLY d 832 " --> pdb=" O LEU d 814 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU d 816 " --> pdb=" O ILE d 830 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE d 830 " --> pdb=" O LEU d 816 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER d 818 " --> pdb=" O TYR d 828 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR d 828 " --> pdb=" O SER d 818 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY d 846 " --> pdb=" O GLU d 865 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU d 865 " --> pdb=" O GLY d 846 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE d 848 " --> pdb=" O GLU d 863 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU d 863 " --> pdb=" O ILE d 848 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL d 850 " --> pdb=" O VAL d 861 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'd' and resid 870 through 876 removed outlier: 3.893A pdb=" N SER d 872 " --> pdb=" O SER d 883 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL d 888 " --> pdb=" O ASN d 904 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN d 904 " --> pdb=" O VAL d 888 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU d 890 " --> pdb=" O GLU d 902 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'd' and resid 911 through 917 removed outlier: 6.826A pdb=" N ALA d 934 " --> pdb=" O GLU d 944 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU d 944 " --> pdb=" O ALA d 934 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'd' and resid 954 through 959 removed outlier: 6.583A pdb=" N ALA d 968 " --> pdb=" O SER d 955 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL d 957 " --> pdb=" O LEU d 966 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU d 966 " --> pdb=" O VAL d 957 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE d 959 " --> pdb=" O ASN d 964 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN d 964 " --> pdb=" O ILE d 959 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN d 973 " --> pdb=" O GLU d 969 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN d 978 " --> pdb=" O GLU d 994 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU d 994 " --> pdb=" O GLN d 978 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'd' and resid 1076 through 1077 Processing sheet with id=AJ6, first strand: chain 'd' and resid 1113 through 1114 Processing sheet with id=AJ7, first strand: chain 'f' and resid 60 through 61 Processing sheet with id=AJ8, first strand: chain 'f' and resid 140 through 142 removed outlier: 5.683A pdb=" N TRP f 175 " --> pdb=" O VAL f 168 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL f 168 " --> pdb=" O TRP f 175 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'f' and resid 206 through 208 2293 hydrogen bonds defined for protein. 6264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 31.36 Time building geometry restraints manager: 12.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10604 1.32 - 1.45: 13600 1.45 - 1.57: 31060 1.57 - 1.70: 184 1.70 - 1.82: 483 Bond restraints: 55931 Sorted by residual: bond pdb=" C ASP A 495 " pdb=" N PHE A 496 " ideal model delta sigma weight residual 1.333 1.295 0.038 1.27e-02 6.20e+03 8.87e+00 bond pdb=" CZ ARG A 460 " pdb=" NH2 ARG A 460 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.85e+00 bond pdb=" C3' DG T 43 " pdb=" O3' DG T 43 " ideal model delta sigma weight residual 1.422 1.341 0.081 3.00e-02 1.11e+03 7.28e+00 bond pdb=" CZ ARG B 975 " pdb=" NH2 ARG B 975 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 7.00e+00 bond pdb=" O3' G P 9 " pdb=" P A P 10 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.50e-02 4.44e+03 6.69e+00 ... (remaining 55926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 75250 3.47 - 6.93: 577 6.93 - 10.40: 93 10.40 - 13.87: 72 13.87 - 17.33: 5 Bond angle restraints: 75997 Sorted by residual: angle pdb=" N ARG d 270 " pdb=" CA ARG d 270 " pdb=" C ARG d 270 " ideal model delta sigma weight residual 108.54 125.87 -17.33 1.41e+00 5.03e-01 1.51e+02 angle pdb=" O3' G P 9 " pdb=" P A P 10 " pdb=" O5' A P 10 " ideal model delta sigma weight residual 104.00 92.59 11.41 1.50e+00 4.44e-01 5.79e+01 angle pdb=" CA ASP A 499 " pdb=" CB ASP A 499 " pdb=" CG ASP A 499 " ideal model delta sigma weight residual 112.60 119.56 -6.96 1.00e+00 1.00e+00 4.84e+01 angle pdb=" N MET d 282 " pdb=" CA MET d 282 " pdb=" C MET d 282 " ideal model delta sigma weight residual 107.71 118.41 -10.70 1.90e+00 2.77e-01 3.17e+01 angle pdb=" N GLY d1066 " pdb=" CA GLY d1066 " pdb=" C GLY d1066 " ideal model delta sigma weight residual 115.27 107.54 7.73 1.41e+00 5.03e-01 3.00e+01 ... (remaining 75992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 32991 34.85 - 69.70: 731 69.70 - 104.55: 77 104.55 - 139.40: 0 139.40 - 174.25: 4 Dihedral angle restraints: 33803 sinusoidal: 14583 harmonic: 19220 Sorted by residual: dihedral pdb=" CA LEU d 152 " pdb=" C LEU d 152 " pdb=" N LYS d 153 " pdb=" CA LYS d 153 " ideal model delta harmonic sigma weight residual 180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA PHE d 155 " pdb=" C PHE d 155 " pdb=" N ASN d 156 " pdb=" CA ASN d 156 " ideal model delta harmonic sigma weight residual -180.00 -151.98 -28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ASP a 35 " pdb=" C ASP a 35 " pdb=" N ARG a 36 " pdb=" CA ARG a 36 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 33800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 7752 0.110 - 0.219: 631 0.219 - 0.329: 41 0.329 - 0.438: 58 0.438 - 0.548: 8 Chirality restraints: 8490 Sorted by residual: chirality pdb=" P DT T 34 " pdb=" OP1 DT T 34 " pdb=" OP2 DT T 34 " pdb=" O5' DT T 34 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" P DC N 12 " pdb=" OP1 DC N 12 " pdb=" OP2 DC N 12 " pdb=" O5' DC N 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" P DT T 40 " pdb=" OP1 DT T 40 " pdb=" OP2 DT T 40 " pdb=" O5' DT T 40 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.17e+00 ... (remaining 8487 not shown) Planarity restraints: 9523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A P 10 " 0.138 2.00e-02 2.50e+03 6.62e-02 1.20e+02 pdb=" N9 A P 10 " 0.007 2.00e-02 2.50e+03 pdb=" C8 A P 10 " -0.018 2.00e-02 2.50e+03 pdb=" N7 A P 10 " -0.060 2.00e-02 2.50e+03 pdb=" C5 A P 10 " -0.054 2.00e-02 2.50e+03 pdb=" C6 A P 10 " 0.016 2.00e-02 2.50e+03 pdb=" N6 A P 10 " 0.095 2.00e-02 2.50e+03 pdb=" N1 A P 10 " 0.043 2.00e-02 2.50e+03 pdb=" C2 A P 10 " -0.020 2.00e-02 2.50e+03 pdb=" N3 A P 10 " -0.076 2.00e-02 2.50e+03 pdb=" C4 A P 10 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 103 " 0.577 9.50e-02 1.11e+02 2.60e-01 4.89e+01 pdb=" NE ARG d 103 " -0.051 2.00e-02 2.50e+03 pdb=" CZ ARG d 103 " 0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG d 103 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG d 103 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 48 " 0.034 2.00e-02 2.50e+03 2.72e-02 2.04e+01 pdb=" N9 DA T 48 " -0.075 2.00e-02 2.50e+03 pdb=" C8 DA T 48 " 0.036 2.00e-02 2.50e+03 pdb=" N7 DA T 48 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA T 48 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA T 48 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA T 48 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA T 48 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA T 48 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA T 48 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 48 " -0.006 2.00e-02 2.50e+03 ... (remaining 9520 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 168 2.50 - 3.10: 38990 3.10 - 3.70: 82430 3.70 - 4.30: 126219 4.30 - 4.90: 206973 Nonbonded interactions: 454780 Sorted by model distance: nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 1.902 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2003 " model vdw 1.910 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.964 2.170 nonbonded pdb=" O3' A P 10 " pdb="MG MG A2003 " model vdw 2.061 2.170 nonbonded pdb=" OD1 ASP b 646 " pdb="MG MG b1501 " model vdw 2.069 2.170 ... (remaining 454775 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.620 Check model and map are aligned: 0.310 Set scattering table: 0.370 Process input model: 124.480 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 55931 Z= 0.583 Angle : 0.983 17.333 75997 Z= 0.528 Chirality : 0.073 0.548 8490 Planarity : 0.010 0.260 9523 Dihedral : 14.541 174.245 21401 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 0.29 % Allowed : 2.39 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.10), residues: 6568 helix: -0.87 (0.10), residues: 2000 sheet: 0.07 (0.13), residues: 1380 loop : -0.45 (0.11), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP f 175 HIS 0.014 0.002 HIS A 809 PHE 0.039 0.004 PHE B 805 TYR 0.039 0.006 TYR H 93 ARG 0.049 0.003 ARG d 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 1532 time to evaluate : 4.474 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: A 238 MET cc_start: 0.7910 (mtp) cc_final: 0.7696 (mtm) REVERT: A 266 MET cc_start: 0.3785 (mmm) cc_final: 0.2408 (mmm) REVERT: A 340 LYS cc_start: 0.8261 (tttt) cc_final: 0.8037 (tttt) REVERT: A 561 MET cc_start: 0.8838 (mtt) cc_final: 0.8628 (mtm) REVERT: A 749 ARG cc_start: 0.7305 (ttp80) cc_final: 0.6974 (ttp80) REVERT: A 845 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7105 (mm-30) REVERT: A 1156 ASP cc_start: 0.6962 (t70) cc_final: 0.5905 (t0) REVERT: A 1214 VAL cc_start: 0.8311 (m) cc_final: 0.8052 (t) REVERT: A 1284 PHE cc_start: 0.8479 (t80) cc_final: 0.8208 (t80) REVERT: A 1341 VAL cc_start: 0.8961 (p) cc_final: 0.8526 (m) REVERT: A 1412 MET cc_start: 0.8714 (ttp) cc_final: 0.8493 (ttp) REVERT: B 255 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7493 (mtp-110) REVERT: B 508 MET cc_start: 0.8896 (mmt) cc_final: 0.8385 (mmt) REVERT: B 641 ASP cc_start: 0.7623 (m-30) cc_final: 0.7363 (m-30) REVERT: B 840 MET cc_start: 0.4208 (mtp) cc_final: 0.4006 (mtp) REVERT: B 954 MET cc_start: 0.9044 (mmm) cc_final: 0.8762 (mmm) REVERT: B 1076 GLU cc_start: 0.6970 (tt0) cc_final: 0.6744 (tt0) REVERT: C 96 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7337 (mm-30) REVERT: C 126 ARG cc_start: 0.7324 (mtp85) cc_final: 0.6978 (mtp85) REVERT: C 157 GLN cc_start: 0.8732 (mt0) cc_final: 0.8489 (mt0) REVERT: C 242 GLU cc_start: 0.8401 (pm20) cc_final: 0.8094 (pm20) REVERT: E 30 GLN cc_start: 0.8249 (tp40) cc_final: 0.7351 (mm-40) REVERT: E 34 ASP cc_start: 0.7662 (p0) cc_final: 0.7322 (p0) REVERT: G 117 MET cc_start: 0.5257 (mtm) cc_final: 0.5052 (mtm) REVERT: M 36 ASP cc_start: 0.7863 (m-30) cc_final: 0.7558 (m-30) REVERT: a 47 ASN cc_start: 0.8175 (m-40) cc_final: 0.7924 (m-40) REVERT: a 52 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7045 (pp20) REVERT: a 103 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6771 (mm-30) REVERT: a 209 SER cc_start: 0.8658 (m) cc_final: 0.8411 (t) REVERT: b 844 VAL cc_start: 0.5368 (t) cc_final: 0.4347 (m) REVERT: b 983 THR cc_start: 0.6020 (m) cc_final: 0.5042 (p) REVERT: b 1269 ASP cc_start: 0.6297 (m-30) cc_final: 0.6046 (t0) REVERT: c 91 LEU cc_start: 0.7660 (mt) cc_final: 0.7029 (mt) REVERT: c 99 LEU cc_start: 0.7780 (mt) cc_final: 0.7379 (mt) REVERT: d 33 ILE cc_start: 0.4897 (mt) cc_final: 0.4647 (mt) REVERT: d 40 GLU cc_start: 0.4491 (OUTLIER) cc_final: 0.4002 (pt0) REVERT: d 189 HIS cc_start: 0.5526 (m-70) cc_final: 0.5311 (m90) REVERT: d 449 MET cc_start: -0.1743 (mtt) cc_final: -0.1947 (mtt) REVERT: d 534 MET cc_start: 0.0788 (mmm) cc_final: 0.0495 (mmm) REVERT: d 873 MET cc_start: 0.8433 (mtm) cc_final: 0.8179 (mtp) REVERT: f 106 GLU cc_start: 0.6090 (tp30) cc_final: 0.5846 (tp30) REVERT: f 207 LEU cc_start: 0.7640 (tp) cc_final: 0.7436 (tp) REVERT: f 251 LEU cc_start: 0.8344 (mt) cc_final: 0.7934 (mt) outliers start: 17 outliers final: 8 residues processed: 1543 average time/residue: 1.5296 time to fit residues: 2914.2923 Evaluate side-chains 1312 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1303 time to evaluate : 4.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain d residue 40 GLU Chi-restraints excluded: chain d residue 54 GLU Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain d residue 1097 PHE Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 178 VAL Chi-restraints excluded: chain f residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 559 optimal weight: 0.5980 chunk 502 optimal weight: 1.9990 chunk 278 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 338 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 chunk 519 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 315 optimal weight: 1.9990 chunk 386 optimal weight: 2.9990 chunk 602 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 288 ASN A 313 HIS A 341 GLN A 502 ASN A 576 GLN A 671 ASN A 731 ASN A 740 GLN A1032 GLN A1077 ASN A1078 GLN A1093 GLN A1420 ASN A1422 GLN B 23 GLN B 56 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 518 HIS B 913 GLN B1025 ASN B1060 HIS C 51 GLN C 177 ASN C 190 ASN C 223 ASN C 232 ASN D 66 ASN D 129 GLN E 19 GLN G 93 ASN H 131 ASN I 32 ASN I 45 GLN I 100 HIS K 2 ASN K 36 ASN K 89 ASN L 26 ASN M 30 ASN a 33 ASN a 94 HIS a 148 HIS a 230 ASN b 525 GLN b 649 HIS b 669 HIS b 679 GLN ** b 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 937 ASN b 943 GLN b1263 HIS d 22 HIS ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 ASN d 105 HIS d 163 HIS ** d 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 663 ASN ** d 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 991 HIS ** d1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d1077 HIS f 78 GLN f 100 HIS f 236 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.199011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.172896 restraints weight = 77346.311| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 1.70 r_work: 0.4210 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4104 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 55931 Z= 0.331 Angle : 0.735 14.532 75997 Z= 0.396 Chirality : 0.049 0.261 8490 Planarity : 0.006 0.080 9523 Dihedral : 12.715 179.377 8323 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.56 % Allowed : 10.45 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.10), residues: 6568 helix: 0.57 (0.11), residues: 2027 sheet: 0.08 (0.13), residues: 1405 loop : -0.13 (0.11), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP b 686 HIS 0.009 0.002 HIS c 73 PHE 0.027 0.002 PHE b 691 TYR 0.043 0.002 TYR d 239 ARG 0.014 0.001 ARG c 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1561 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1412 time to evaluate : 4.540 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: A 219 GLU cc_start: 0.6329 (tp30) cc_final: 0.6076 (tp30) REVERT: A 238 MET cc_start: 0.7724 (mtp) cc_final: 0.7517 (mtm) REVERT: A 266 MET cc_start: 0.4157 (mmm) cc_final: 0.2696 (mmm) REVERT: A 346 LYS cc_start: 0.7673 (ptpt) cc_final: 0.7439 (ttpp) REVERT: A 418 TYR cc_start: 0.8642 (m-80) cc_final: 0.8387 (m-80) REVERT: A 561 MET cc_start: 0.9006 (mtt) cc_final: 0.8680 (mtt) REVERT: A 749 ARG cc_start: 0.7413 (ttp80) cc_final: 0.7021 (ttp80) REVERT: A 845 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6937 (mm-30) REVERT: A 957 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7652 (mm-30) REVERT: A 960 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7855 (ttm170) REVERT: A 1156 ASP cc_start: 0.7234 (t70) cc_final: 0.6958 (t0) REVERT: A 1221 MET cc_start: 0.7937 (mmm) cc_final: 0.7690 (tpt) REVERT: A 1412 MET cc_start: 0.8719 (ttp) cc_final: 0.8431 (ttp) REVERT: A 1422 GLN cc_start: 0.8093 (mt0) cc_final: 0.7783 (mt0) REVERT: B 61 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7240 (t0) REVERT: B 294 ASP cc_start: 0.7606 (t0) cc_final: 0.7391 (t70) REVERT: B 500 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7958 (mm110) REVERT: B 918 PHE cc_start: 0.8408 (t80) cc_final: 0.8155 (t80) REVERT: B 1071 ASN cc_start: 0.8205 (p0) cc_final: 0.7988 (p0) REVERT: C 96 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7541 (mm-30) REVERT: C 106 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7600 (ttm170) REVERT: C 126 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7861 (mtp85) REVERT: C 157 GLN cc_start: 0.8610 (mt0) cc_final: 0.8388 (mt0) REVERT: C 254 LYS cc_start: 0.8068 (tttp) cc_final: 0.7865 (tttp) REVERT: E 30 GLN cc_start: 0.8222 (tp40) cc_final: 0.7428 (mm-40) REVERT: E 34 ASP cc_start: 0.7838 (p0) cc_final: 0.7480 (p0) REVERT: H 42 ASP cc_start: 0.8372 (m-30) cc_final: 0.8077 (m-30) REVERT: H 45 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8618 (pp) REVERT: K 110 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7773 (mptp) REVERT: L 39 CYS cc_start: 0.7831 (p) cc_final: 0.7565 (p) REVERT: b 594 VAL cc_start: 0.4029 (OUTLIER) cc_final: 0.3432 (m) REVERT: b 620 ILE cc_start: 0.5451 (OUTLIER) cc_final: 0.4949 (mt) REVERT: b 872 GLU cc_start: 0.4217 (OUTLIER) cc_final: 0.3733 (tm-30) REVERT: c 49 GLN cc_start: 0.8335 (tp-100) cc_final: 0.8095 (tp40) REVERT: c 52 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6904 (mm-40) REVERT: c 91 LEU cc_start: 0.8404 (mt) cc_final: 0.7639 (mt) REVERT: c 99 LEU cc_start: 0.8252 (mt) cc_final: 0.7779 (mt) REVERT: c 110 ARG cc_start: 0.7700 (ttm170) cc_final: 0.6981 (ttm170) REVERT: c 139 ARG cc_start: 0.7374 (ttt180) cc_final: 0.7130 (ttp-170) REVERT: c 669 ARG cc_start: 0.8296 (mtt90) cc_final: 0.8090 (ttm-80) REVERT: d 81 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7484 (p) REVERT: d 130 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6962 (ptp) REVERT: d 391 ARG cc_start: 0.7325 (ptm160) cc_final: 0.6961 (ptm160) REVERT: d 840 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6389 (mt-10) REVERT: d 873 MET cc_start: 0.8177 (mtm) cc_final: 0.7769 (mtp) REVERT: d 906 TYR cc_start: 0.8517 (m-80) cc_final: 0.8275 (m-80) REVERT: f 41 SER cc_start: 0.7991 (p) cc_final: 0.7390 (m) REVERT: f 200 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7311 (ttm110) outliers start: 149 outliers final: 49 residues processed: 1466 average time/residue: 1.5704 time to fit residues: 2837.1580 Evaluate side-chains 1341 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 1283 time to evaluate : 4.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain a residue 254 THR Chi-restraints excluded: chain b residue 594 VAL Chi-restraints excluded: chain b residue 620 ILE Chi-restraints excluded: chain b residue 730 CYS Chi-restraints excluded: chain b residue 858 VAL Chi-restraints excluded: chain b residue 872 GLU Chi-restraints excluded: chain b residue 909 VAL Chi-restraints excluded: chain b residue 1025 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 80 LEU Chi-restraints excluded: chain d residue 81 THR Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 130 MET Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain d residue 1061 VAL Chi-restraints excluded: chain d residue 1083 GLU Chi-restraints excluded: chain f residue 62 ARG Chi-restraints excluded: chain f residue 126 GLN Chi-restraints excluded: chain f residue 250 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 299 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 431 optimal weight: 1.9990 chunk 560 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 487 optimal weight: 0.3980 chunk 536 optimal weight: 0.7980 chunk 311 optimal weight: 0.6980 chunk 534 optimal weight: 0.5980 chunk 171 optimal weight: 0.0570 chunk 287 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 288 ASN A 576 GLN A 731 ASN B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 350 HIS B 518 HIS B1068 GLN B1160 GLN C 5 ASN C 177 ASN C 223 ASN E 43 GLN H 44 ASN I 32 ASN I 45 GLN L 26 ASN M 30 ASN a 230 ASN a 357 ASN b 679 GLN b 760 ASN b 762 GLN b 922 ASN b 943 GLN c 141 ASN d 36 ASN d 163 HIS d 355 ASN ** d 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 392 ASN d 711 HIS d 759 GLN d 970 ASN d 993 GLN d1070 HIS f 64 GLN f 100 HIS f 236 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.194547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.167255 restraints weight = 76525.972| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 1.76 r_work: 0.4128 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3999 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 55931 Z= 0.207 Angle : 0.576 13.558 75997 Z= 0.309 Chirality : 0.045 0.244 8490 Planarity : 0.004 0.047 9523 Dihedral : 12.195 177.271 8309 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.41 % Allowed : 13.51 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.10), residues: 6568 helix: 1.05 (0.12), residues: 2048 sheet: 0.11 (0.13), residues: 1416 loop : 0.02 (0.11), residues: 3104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 686 HIS 0.013 0.001 HIS G 4 PHE 0.027 0.002 PHE D 61 TYR 0.021 0.001 TYR d 245 ARG 0.017 0.001 ARG b 683 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 1351 time to evaluate : 4.589 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: A 266 MET cc_start: 0.3946 (mmm) cc_final: 0.2629 (mmm) REVERT: A 418 TYR cc_start: 0.8640 (m-80) cc_final: 0.8305 (m-80) REVERT: A 561 MET cc_start: 0.9029 (mtt) cc_final: 0.8647 (mtt) REVERT: A 749 ARG cc_start: 0.7389 (ttp80) cc_final: 0.7047 (ttp80) REVERT: A 845 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7030 (mm-30) REVERT: A 957 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 960 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.7864 (ttm170) REVERT: A 1156 ASP cc_start: 0.7313 (t70) cc_final: 0.7037 (t0) REVERT: A 1221 MET cc_start: 0.8079 (mmm) cc_final: 0.7780 (tpt) REVERT: A 1306 LYS cc_start: 0.8251 (tptp) cc_final: 0.8045 (tptp) REVERT: A 1412 MET cc_start: 0.8798 (ttp) cc_final: 0.8540 (ttp) REVERT: A 1422 GLN cc_start: 0.8087 (mt0) cc_final: 0.7764 (mt0) REVERT: B 294 ASP cc_start: 0.7598 (t0) cc_final: 0.7338 (t70) REVERT: B 500 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7931 (mm110) REVERT: B 645 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: B 702 MET cc_start: 0.9196 (mmp) cc_final: 0.8974 (mmp) REVERT: B 918 PHE cc_start: 0.8373 (t80) cc_final: 0.8111 (t80) REVERT: B 1071 ASN cc_start: 0.8247 (p0) cc_final: 0.7996 (p0) REVERT: B 1076 GLU cc_start: 0.7611 (tt0) cc_final: 0.7324 (tt0) REVERT: C 126 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7833 (mtp85) REVERT: E 30 GLN cc_start: 0.8260 (tp40) cc_final: 0.7589 (mm-40) REVERT: E 34 ASP cc_start: 0.7920 (p0) cc_final: 0.7645 (p0) REVERT: G 59 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8350 (mt) REVERT: H 45 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8632 (pp) REVERT: K 110 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7812 (mptp) REVERT: L 39 CYS cc_start: 0.7737 (p) cc_final: 0.7465 (p) REVERT: b 551 TYR cc_start: 0.6343 (t80) cc_final: 0.5763 (t80) REVERT: c 27 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7376 (mm-30) REVERT: c 49 GLN cc_start: 0.8233 (tp-100) cc_final: 0.8015 (tp40) REVERT: c 52 GLN cc_start: 0.7277 (mm-40) cc_final: 0.6892 (mm-40) REVERT: c 91 LEU cc_start: 0.8354 (mt) cc_final: 0.7851 (mt) REVERT: c 99 LEU cc_start: 0.8300 (mt) cc_final: 0.7667 (mt) REVERT: c 110 ARG cc_start: 0.7575 (ttm170) cc_final: 0.6906 (ttm170) REVERT: c 139 ARG cc_start: 0.7363 (ttt180) cc_final: 0.7089 (ttt180) REVERT: d 709 LYS cc_start: 0.7487 (pptt) cc_final: 0.7108 (pptt) REVERT: d 873 MET cc_start: 0.8272 (mtm) cc_final: 0.7817 (mtp) REVERT: d 933 LEU cc_start: 0.8372 (mt) cc_final: 0.8154 (mt) REVERT: d 1134 GLU cc_start: 0.7433 (tm-30) cc_final: 0.6973 (tp30) REVERT: e 5 LEU cc_start: 0.7669 (mt) cc_final: 0.7338 (mp) outliers start: 140 outliers final: 50 residues processed: 1404 average time/residue: 1.6050 time to fit residues: 2767.5253 Evaluate side-chains 1354 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 1299 time to evaluate : 4.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain a residue 167 LYS Chi-restraints excluded: chain a residue 254 THR Chi-restraints excluded: chain b residue 702 VAL Chi-restraints excluded: chain b residue 730 CYS Chi-restraints excluded: chain b residue 843 VAL Chi-restraints excluded: chain b residue 858 VAL Chi-restraints excluded: chain b residue 909 VAL Chi-restraints excluded: chain b residue 955 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain d residue 354 THR Chi-restraints excluded: chain d residue 895 THR Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain d residue 1083 GLU Chi-restraints excluded: chain f residue 126 GLN Chi-restraints excluded: chain f residue 193 GLN Chi-restraints excluded: chain f residue 250 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 86 optimal weight: 1.9990 chunk 381 optimal weight: 0.0370 chunk 441 optimal weight: 0.9980 chunk 300 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 458 optimal weight: 0.6980 chunk 350 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 447 optimal weight: 0.9980 chunk 538 optimal weight: 0.1980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 288 ASN A 576 GLN A 731 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 518 HIS B1068 GLN B1115 GLN C 157 GLN C 177 ASN C 223 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN E 43 GLN I 32 ASN I 45 GLN K 2 ASN L 26 ASN M 30 ASN a 47 ASN a 230 ASN a 343 GLN a 357 ASN b 852 HIS b 854 GLN b 976 GLN c 140 HIS d 163 HIS d 374 GLN d 759 GLN d 970 ASN d1049 ASN d1056 ASN e 12 ASN e 15 ASN f 64 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.189241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.158608 restraints weight = 74052.318| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.50 r_work: 0.4063 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 55931 Z= 0.221 Angle : 0.591 15.711 75997 Z= 0.314 Chirality : 0.045 0.201 8490 Planarity : 0.005 0.056 9523 Dihedral : 12.047 176.614 8307 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.87 % Allowed : 14.60 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.10), residues: 6568 helix: 1.16 (0.12), residues: 2049 sheet: 0.15 (0.13), residues: 1420 loop : 0.03 (0.11), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP f 174 HIS 0.008 0.001 HIS b 579 PHE 0.028 0.002 PHE M 57 TYR 0.024 0.002 TYR B 388 ARG 0.009 0.001 ARG f 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1540 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1373 time to evaluate : 4.638 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: A 16 ARG cc_start: 0.7674 (mtm180) cc_final: 0.7472 (mtm180) REVERT: A 266 MET cc_start: 0.3858 (mmm) cc_final: 0.2493 (mmm) REVERT: A 418 TYR cc_start: 0.8580 (m-80) cc_final: 0.8227 (m-80) REVERT: A 561 MET cc_start: 0.8976 (mtt) cc_final: 0.8627 (mtt) REVERT: A 673 GLN cc_start: 0.8600 (mt0) cc_final: 0.8398 (mt0) REVERT: A 749 ARG cc_start: 0.7276 (ttp80) cc_final: 0.6939 (ttp80) REVERT: A 769 MET cc_start: 0.8889 (mtm) cc_final: 0.8537 (mtp) REVERT: A 845 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7044 (mm-30) REVERT: A 951 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: A 957 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 960 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7807 (ttm170) REVERT: A 1217 ASP cc_start: 0.7136 (p0) cc_final: 0.6917 (p0) REVERT: A 1221 MET cc_start: 0.8122 (mmm) cc_final: 0.7778 (tpt) REVERT: A 1233 GLU cc_start: 0.8050 (tp30) cc_final: 0.7837 (tp30) REVERT: A 1306 LYS cc_start: 0.8117 (tptp) cc_final: 0.7824 (tptp) REVERT: A 1412 MET cc_start: 0.8750 (ttp) cc_final: 0.8451 (ttp) REVERT: A 1422 GLN cc_start: 0.7973 (mt0) cc_final: 0.7686 (mt0) REVERT: B 280 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7797 (p) REVERT: B 497 LYS cc_start: 0.7967 (tptp) cc_final: 0.7680 (tptp) REVERT: B 500 GLN cc_start: 0.8260 (mm110) cc_final: 0.7879 (mm110) REVERT: B 508 MET cc_start: 0.8865 (mmt) cc_final: 0.7803 (mmt) REVERT: B 645 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: B 702 MET cc_start: 0.9178 (mmp) cc_final: 0.8907 (mmp) REVERT: B 890 ARG cc_start: 0.6932 (ttp-110) cc_final: 0.6724 (ttp-110) REVERT: B 1071 ASN cc_start: 0.8271 (p0) cc_final: 0.8014 (p0) REVERT: B 1076 GLU cc_start: 0.7543 (tt0) cc_final: 0.7282 (tt0) REVERT: C 123 ASN cc_start: 0.8037 (p0) cc_final: 0.7837 (p0) REVERT: C 126 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7570 (mtp85) REVERT: D 87 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5312 (mt) REVERT: E 30 GLN cc_start: 0.8240 (tp40) cc_final: 0.7683 (mm-40) REVERT: E 34 ASP cc_start: 0.7808 (p0) cc_final: 0.7562 (p0) REVERT: E 202 ARG cc_start: 0.8602 (ttm110) cc_final: 0.8288 (ttm110) REVERT: G 59 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8376 (mt) REVERT: H 45 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8618 (pp) REVERT: J 1 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7962 (mtm) REVERT: K 110 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7694 (mptp) REVERT: a 52 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7320 (pp20) REVERT: a 210 ARG cc_start: 0.8147 (tpp-160) cc_final: 0.7923 (tpp-160) REVERT: b 587 THR cc_start: 0.6329 (m) cc_final: 0.5182 (p) REVERT: b 933 ASP cc_start: 0.8203 (p0) cc_final: 0.7963 (p0) REVERT: c 56 GLU cc_start: 0.7091 (mp0) cc_final: 0.6689 (mp0) REVERT: c 77 MET cc_start: 0.7929 (tmm) cc_final: 0.7597 (tmm) REVERT: d 873 MET cc_start: 0.8274 (mtm) cc_final: 0.7827 (mtp) REVERT: d 933 LEU cc_start: 0.8406 (mt) cc_final: 0.8172 (mt) REVERT: e 5 LEU cc_start: 0.7959 (mt) cc_final: 0.7703 (mp) outliers start: 167 outliers final: 67 residues processed: 1430 average time/residue: 1.5749 time to fit residues: 2768.6666 Evaluate side-chains 1376 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 1300 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 751 LYS Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 167 LYS Chi-restraints excluded: chain a residue 178 CYS Chi-restraints excluded: chain a residue 254 THR Chi-restraints excluded: chain b residue 684 GLU Chi-restraints excluded: chain b residue 702 VAL Chi-restraints excluded: chain b residue 843 VAL Chi-restraints excluded: chain b residue 858 VAL Chi-restraints excluded: chain b residue 909 VAL Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 234 GLN Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 354 THR Chi-restraints excluded: chain d residue 430 VAL Chi-restraints excluded: chain d residue 1041 THR Chi-restraints excluded: chain f residue 131 SER Chi-restraints excluded: chain f residue 193 GLN Chi-restraints excluded: chain f residue 250 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 8 optimal weight: 2.9990 chunk 468 optimal weight: 0.9990 chunk 371 optimal weight: 4.9990 chunk 458 optimal weight: 0.4980 chunk 382 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 570 optimal weight: 30.0000 chunk 659 optimal weight: 0.9990 chunk 564 optimal weight: 50.0000 chunk 282 optimal weight: 0.8980 chunk 581 optimal weight: 40.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 296 ASN A 576 GLN A 673 GLN A 731 ASN A 804 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN C 157 GLN C 177 ASN C 223 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN E 174 GLN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN H 46 GLN I 45 GLN K 2 ASN L 26 ASN M 30 ASN a 47 ASN a 98 HIS a 230 ASN a 241 ASN a 343 GLN a 357 ASN b 522 HIS b 524 GLN b 760 ASN b 976 GLN d 109 GLN d 163 HIS d 240 HIS d 241 ASN d 261 HIS d 332 GLN d 970 ASN d 978 GLN d 990 GLN d1056 ASN f 64 GLN f 78 GLN f 236 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.182956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.151776 restraints weight = 71565.873| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.46 r_work: 0.3963 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 55931 Z= 0.369 Angle : 0.663 13.334 75997 Z= 0.351 Chirality : 0.048 0.250 8490 Planarity : 0.005 0.065 9523 Dihedral : 12.125 177.013 8307 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.25 % Allowed : 15.28 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 6568 helix: 0.98 (0.11), residues: 2048 sheet: 0.09 (0.13), residues: 1446 loop : -0.09 (0.11), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP b 468 HIS 0.017 0.002 HIS D 38 PHE 0.042 0.002 PHE f 104 TYR 0.041 0.002 TYR B 388 ARG 0.015 0.001 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1334 time to evaluate : 4.701 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: A 20 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7790 (ptm-80) REVERT: A 266 MET cc_start: 0.3729 (mmm) cc_final: 0.2385 (mmm) REVERT: A 418 TYR cc_start: 0.8676 (m-80) cc_final: 0.8349 (m-80) REVERT: A 421 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7978 (mtt180) REVERT: A 561 MET cc_start: 0.8982 (mtt) cc_final: 0.8625 (mtt) REVERT: A 749 ARG cc_start: 0.7280 (ttp80) cc_final: 0.7054 (ttp80) REVERT: A 845 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7082 (mm-30) REVERT: A 951 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: A 957 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 960 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7838 (ttm170) REVERT: A 1143 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8641 (mt) REVERT: A 1215 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7285 (mt-10) REVERT: A 1221 MET cc_start: 0.8109 (mmm) cc_final: 0.7824 (tpt) REVERT: A 1228 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7691 (mtm) REVERT: A 1233 GLU cc_start: 0.8011 (tp30) cc_final: 0.7770 (tp30) REVERT: A 1284 PHE cc_start: 0.8672 (t80) cc_final: 0.8450 (t80) REVERT: A 1306 LYS cc_start: 0.8112 (tptp) cc_final: 0.7795 (tptp) REVERT: A 1422 GLN cc_start: 0.8003 (mt0) cc_final: 0.7722 (mt0) REVERT: A 1454 VAL cc_start: 0.8720 (m) cc_final: 0.8497 (t) REVERT: B 225 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7785 (tt) REVERT: B 381 GLU cc_start: 0.7812 (mp0) cc_final: 0.7611 (mp0) REVERT: B 497 LYS cc_start: 0.7951 (tptp) cc_final: 0.7664 (tptp) REVERT: B 508 MET cc_start: 0.8864 (mmt) cc_final: 0.7897 (mmt) REVERT: B 638 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7753 (ptt-90) REVERT: B 645 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: B 702 MET cc_start: 0.9162 (mmp) cc_final: 0.8931 (mmp) REVERT: B 840 MET cc_start: 0.4280 (OUTLIER) cc_final: 0.3772 (ttp) REVERT: B 1071 ASN cc_start: 0.8254 (p0) cc_final: 0.8001 (p0) REVERT: B 1076 GLU cc_start: 0.7529 (tt0) cc_final: 0.7182 (tt0) REVERT: C 126 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7518 (mtp85) REVERT: E 30 GLN cc_start: 0.8253 (tp40) cc_final: 0.7698 (mm-40) REVERT: E 34 ASP cc_start: 0.7789 (p0) cc_final: 0.7572 (p0) REVERT: H 45 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8541 (pp) REVERT: J 1 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8026 (mtm) REVERT: K 110 LYS cc_start: 0.7868 (tptp) cc_final: 0.7622 (mptp) REVERT: a 52 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7551 (pp20) REVERT: b 779 PHE cc_start: 0.7146 (t80) cc_final: 0.6895 (t80) REVERT: c 12 LEU cc_start: 0.7911 (mm) cc_final: 0.7599 (tp) REVERT: c 77 MET cc_start: 0.7954 (tmm) cc_final: 0.7630 (tmm) REVERT: c 110 ARG cc_start: 0.7713 (ttm170) cc_final: 0.7314 (ttm170) REVERT: d 64 MET cc_start: 0.8417 (ttp) cc_final: 0.8113 (ttp) REVERT: d 130 MET cc_start: 0.8572 (ptp) cc_final: 0.8102 (ptp) REVERT: d 693 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6503 (mp) REVERT: d 709 LYS cc_start: 0.7485 (pptt) cc_final: 0.6895 (pptt) REVERT: d 873 MET cc_start: 0.8448 (mtm) cc_final: 0.8071 (mtp) outliers start: 189 outliers final: 83 residues processed: 1397 average time/residue: 1.6027 time to fit residues: 2745.1531 Evaluate side-chains 1394 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1298 time to evaluate : 4.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 167 LYS Chi-restraints excluded: chain a residue 174 LYS Chi-restraints excluded: chain b residue 676 SER Chi-restraints excluded: chain b residue 692 ILE Chi-restraints excluded: chain b residue 843 VAL Chi-restraints excluded: chain b residue 909 VAL Chi-restraints excluded: chain c residue 17 GLU Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 667 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 16 ASN Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 235 GLU Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain d residue 430 VAL Chi-restraints excluded: chain d residue 693 LEU Chi-restraints excluded: chain d residue 801 VAL Chi-restraints excluded: chain d residue 1041 THR Chi-restraints excluded: chain d residue 1134 GLU Chi-restraints excluded: chain f residue 126 GLN Chi-restraints excluded: chain f residue 250 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 356 optimal weight: 0.9980 chunk 582 optimal weight: 20.0000 chunk 468 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 444 optimal weight: 7.9990 chunk 302 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 369 optimal weight: 0.1980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 576 GLN A 673 GLN A 731 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 518 HIS B1068 GLN B1145 GLN B1160 GLN C 5 ASN C 157 GLN C 177 ASN G 4 HIS I 45 GLN K 2 ASN L 26 ASN M 30 ASN a 9 GLN a 47 ASN a 230 ASN a 357 ASN b 649 HIS b 922 ASN b 956 GLN ** b 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 HIS d 183 GLN d 332 GLN d 663 ASN d 970 ASN d 990 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.182470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.150529 restraints weight = 71559.418| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.49 r_work: 0.3959 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 55931 Z= 0.251 Angle : 0.587 18.903 75997 Z= 0.310 Chirality : 0.045 0.208 8490 Planarity : 0.004 0.050 9523 Dihedral : 12.006 179.163 8307 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.58 % Allowed : 16.78 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.10), residues: 6568 helix: 1.19 (0.12), residues: 2036 sheet: 0.14 (0.13), residues: 1430 loop : -0.10 (0.11), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 468 HIS 0.007 0.001 HIS D 38 PHE 0.029 0.002 PHE M 57 TYR 0.028 0.002 TYR B 388 ARG 0.012 0.001 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1321 time to evaluate : 4.612 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: A 16 ARG cc_start: 0.7545 (mtm180) cc_final: 0.7268 (mtm180) REVERT: A 20 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7738 (ptm-80) REVERT: A 241 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7429 (ttp80) REVERT: A 266 MET cc_start: 0.3802 (mmm) cc_final: 0.1933 (mmm) REVERT: A 418 TYR cc_start: 0.8676 (m-80) cc_final: 0.8391 (m-80) REVERT: A 561 MET cc_start: 0.8995 (mtt) cc_final: 0.8675 (mtt) REVERT: A 769 MET cc_start: 0.8832 (mtm) cc_final: 0.8592 (mtp) REVERT: A 845 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7123 (mm-30) REVERT: A 951 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: A 960 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7848 (ttm170) REVERT: A 1143 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8595 (mt) REVERT: A 1160 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7672 (ttm-80) REVERT: A 1221 MET cc_start: 0.8041 (mmm) cc_final: 0.7753 (tpt) REVERT: A 1228 MET cc_start: 0.7943 (mmm) cc_final: 0.6776 (mtm) REVERT: A 1233 GLU cc_start: 0.8020 (tp30) cc_final: 0.7790 (tp30) REVERT: A 1284 PHE cc_start: 0.8576 (t80) cc_final: 0.8367 (t80) REVERT: A 1306 LYS cc_start: 0.8071 (tptp) cc_final: 0.7741 (tptp) REVERT: A 1422 GLN cc_start: 0.7773 (mt0) cc_final: 0.7462 (mt0) REVERT: A 1454 VAL cc_start: 0.8684 (m) cc_final: 0.8475 (t) REVERT: A 1478 GLU cc_start: 0.7871 (tp30) cc_final: 0.7406 (tp30) REVERT: B 381 GLU cc_start: 0.7830 (mp0) cc_final: 0.7626 (mp0) REVERT: B 497 LYS cc_start: 0.7910 (tptp) cc_final: 0.7605 (tptp) REVERT: B 508 MET cc_start: 0.8873 (mmt) cc_final: 0.7823 (mmt) REVERT: B 638 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7740 (ptt-90) REVERT: B 645 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: B 702 MET cc_start: 0.9176 (mmp) cc_final: 0.8910 (mmp) REVERT: B 840 MET cc_start: 0.4557 (OUTLIER) cc_final: 0.4247 (ttp) REVERT: B 890 ARG cc_start: 0.6944 (ttp-110) cc_final: 0.6685 (ttp-110) REVERT: B 1071 ASN cc_start: 0.8274 (p0) cc_final: 0.8031 (p0) REVERT: B 1076 GLU cc_start: 0.7498 (tt0) cc_final: 0.7167 (tt0) REVERT: C 126 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7654 (mtp85) REVERT: E 30 GLN cc_start: 0.8179 (tp40) cc_final: 0.7769 (tp-100) REVERT: F 80 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.7854 (mmm) REVERT: H 45 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8550 (pp) REVERT: K 110 LYS cc_start: 0.7896 (tptp) cc_final: 0.7671 (mptp) REVERT: a 52 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7539 (pp20) REVERT: b 779 PHE cc_start: 0.7858 (t80) cc_final: 0.7491 (t80) REVERT: b 876 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6820 (mpp80) REVERT: c 1 MET cc_start: 0.5670 (tmm) cc_final: 0.5395 (tmm) REVERT: c 12 LEU cc_start: 0.7815 (mm) cc_final: 0.7570 (tp) REVERT: c 68 LEU cc_start: 0.8780 (mt) cc_final: 0.8073 (tm) REVERT: c 77 MET cc_start: 0.7840 (tmm) cc_final: 0.7511 (tmm) REVERT: c 139 ARG cc_start: 0.7495 (ttt180) cc_final: 0.6937 (ttt180) REVERT: c 669 ARG cc_start: 0.8250 (mtt90) cc_final: 0.7955 (mtt90) REVERT: d 234 GLN cc_start: 0.8145 (tt0) cc_final: 0.7944 (mt0) REVERT: d 299 ASP cc_start: 0.7188 (t0) cc_final: 0.6963 (t70) REVERT: d 652 CYS cc_start: 0.3147 (OUTLIER) cc_final: 0.1741 (t) REVERT: d 693 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6453 (mp) REVERT: d 709 LYS cc_start: 0.7785 (pptt) cc_final: 0.7011 (pptt) REVERT: d 873 MET cc_start: 0.8401 (mtm) cc_final: 0.7948 (mtp) outliers start: 150 outliers final: 76 residues processed: 1374 average time/residue: 1.6104 time to fit residues: 2703.4790 Evaluate side-chains 1380 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1292 time to evaluate : 4.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 167 LYS Chi-restraints excluded: chain a residue 174 LYS Chi-restraints excluded: chain a residue 348 GLU Chi-restraints excluded: chain b residue 631 MET Chi-restraints excluded: chain b residue 752 MET Chi-restraints excluded: chain b residue 843 VAL Chi-restraints excluded: chain b residue 848 LEU Chi-restraints excluded: chain b residue 876 ARG Chi-restraints excluded: chain b residue 909 VAL Chi-restraints excluded: chain c residue 667 THR Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 430 VAL Chi-restraints excluded: chain d residue 437 MET Chi-restraints excluded: chain d residue 652 CYS Chi-restraints excluded: chain d residue 693 LEU Chi-restraints excluded: chain d residue 801 VAL Chi-restraints excluded: chain d residue 895 THR Chi-restraints excluded: chain d residue 1041 THR Chi-restraints excluded: chain d residue 1134 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain f residue 126 GLN Chi-restraints excluded: chain f residue 193 GLN Chi-restraints excluded: chain f residue 250 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 302 optimal weight: 0.9980 chunk 425 optimal weight: 0.9990 chunk 295 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 545 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 341 GLN A 576 GLN A 731 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 518 HIS B 980 HIS B1068 GLN B1101 GLN C 55 ASN C 157 GLN C 177 ASN D 38 HIS H 44 ASN I 45 GLN L 26 ASN M 30 ASN a 9 GLN a 47 ASN a 230 ASN a 343 GLN a 357 ASN b 632 GLN b 760 ASN b 956 GLN ** b 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 HIS d 759 GLN d 970 ASN d 993 GLN f 236 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.181345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.149393 restraints weight = 71056.698| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.50 r_work: 0.3942 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 55931 Z= 0.260 Angle : 0.594 12.971 75997 Z= 0.314 Chirality : 0.045 0.260 8490 Planarity : 0.004 0.060 9523 Dihedral : 12.013 178.190 8307 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.63 % Allowed : 17.23 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 6568 helix: 1.21 (0.12), residues: 2034 sheet: 0.13 (0.13), residues: 1433 loop : -0.09 (0.11), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 468 HIS 0.007 0.001 HIS D 38 PHE 0.027 0.002 PHE M 57 TYR 0.024 0.002 TYR b 638 ARG 0.014 0.001 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1465 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 1312 time to evaluate : 4.584 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: A 20 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7755 (ptm-80) REVERT: A 145 TYR cc_start: 0.8431 (t80) cc_final: 0.8203 (t80) REVERT: A 266 MET cc_start: 0.3786 (mmm) cc_final: 0.1983 (mmm) REVERT: A 418 TYR cc_start: 0.8669 (m-80) cc_final: 0.8379 (m-80) REVERT: A 421 ARG cc_start: 0.8471 (mtt180) cc_final: 0.8112 (mtt90) REVERT: A 561 MET cc_start: 0.8983 (mtt) cc_final: 0.8668 (mtt) REVERT: A 769 MET cc_start: 0.8818 (mtm) cc_final: 0.8585 (mtp) REVERT: A 845 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7098 (mm-30) REVERT: A 951 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 960 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7864 (ttm170) REVERT: A 1143 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 1215 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7345 (mt-10) REVERT: A 1221 MET cc_start: 0.8015 (mmm) cc_final: 0.7740 (tpt) REVERT: A 1228 MET cc_start: 0.8006 (mmm) cc_final: 0.6804 (mtm) REVERT: A 1233 GLU cc_start: 0.8004 (tp30) cc_final: 0.7787 (tp30) REVERT: A 1284 PHE cc_start: 0.8617 (t80) cc_final: 0.8394 (t80) REVERT: A 1306 LYS cc_start: 0.8106 (tptp) cc_final: 0.7810 (tptp) REVERT: A 1422 GLN cc_start: 0.7703 (mt0) cc_final: 0.7393 (mt0) REVERT: A 1454 VAL cc_start: 0.8666 (m) cc_final: 0.8427 (t) REVERT: A 1478 GLU cc_start: 0.7891 (tp30) cc_final: 0.7463 (tp30) REVERT: B 225 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7780 (tt) REVERT: B 381 GLU cc_start: 0.7881 (mp0) cc_final: 0.7655 (mp0) REVERT: B 497 LYS cc_start: 0.7839 (tptp) cc_final: 0.7542 (tptp) REVERT: B 508 MET cc_start: 0.8865 (mmt) cc_final: 0.7819 (mmt) REVERT: B 638 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7788 (ptt-90) REVERT: B 645 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: B 702 MET cc_start: 0.9153 (mmp) cc_final: 0.8850 (mmp) REVERT: B 744 MET cc_start: 0.8559 (mmt) cc_final: 0.7924 (mmt) REVERT: B 890 ARG cc_start: 0.6980 (ttp-110) cc_final: 0.6683 (ttp-110) REVERT: B 1071 ASN cc_start: 0.8260 (p0) cc_final: 0.8029 (p0) REVERT: B 1076 GLU cc_start: 0.7471 (tt0) cc_final: 0.7113 (tt0) REVERT: C 126 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7539 (mtp85) REVERT: F 80 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7848 (mmm) REVERT: G 164 MET cc_start: 0.6970 (mmm) cc_final: 0.6548 (mpm) REVERT: H 45 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8539 (pp) REVERT: K 110 LYS cc_start: 0.7871 (tptp) cc_final: 0.7651 (mptp) REVERT: a 52 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7524 (pp20) REVERT: b 876 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6887 (mpp80) REVERT: c 1 MET cc_start: 0.5725 (tmm) cc_final: 0.5477 (tmm) REVERT: c 12 LEU cc_start: 0.8036 (mm) cc_final: 0.7767 (tp) REVERT: c 68 LEU cc_start: 0.8773 (mt) cc_final: 0.8055 (tm) REVERT: c 77 MET cc_start: 0.7893 (tmm) cc_final: 0.7509 (tmm) REVERT: c 110 ARG cc_start: 0.7759 (ttm170) cc_final: 0.7252 (ttm170) REVERT: c 669 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7930 (mtt90) REVERT: d 57 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8347 (mmt) REVERT: d 652 CYS cc_start: 0.2914 (OUTLIER) cc_final: 0.1429 (t) REVERT: d 693 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6693 (mp) REVERT: d 709 LYS cc_start: 0.7881 (pptt) cc_final: 0.7217 (pptt) REVERT: d 873 MET cc_start: 0.8449 (mtm) cc_final: 0.8020 (mtp) outliers start: 153 outliers final: 89 residues processed: 1370 average time/residue: 1.5974 time to fit residues: 2674.6282 Evaluate side-chains 1389 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 1287 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 174 LYS Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 296 LYS Chi-restraints excluded: chain a residue 348 GLU Chi-restraints excluded: chain b residue 631 MET Chi-restraints excluded: chain b residue 676 SER Chi-restraints excluded: chain b residue 752 MET Chi-restraints excluded: chain b residue 843 VAL Chi-restraints excluded: chain b residue 848 LEU Chi-restraints excluded: chain b residue 876 ARG Chi-restraints excluded: chain b residue 897 LEU Chi-restraints excluded: chain b residue 909 VAL Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 667 THR Chi-restraints excluded: chain d residue 16 ASN Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 70 LYS Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain d residue 430 VAL Chi-restraints excluded: chain d residue 437 MET Chi-restraints excluded: chain d residue 652 CYS Chi-restraints excluded: chain d residue 693 LEU Chi-restraints excluded: chain d residue 801 VAL Chi-restraints excluded: chain d residue 895 THR Chi-restraints excluded: chain d residue 1041 THR Chi-restraints excluded: chain d residue 1053 ASP Chi-restraints excluded: chain d residue 1083 GLU Chi-restraints excluded: chain d residue 1134 GLU Chi-restraints excluded: chain f residue 126 GLN Chi-restraints excluded: chain f residue 193 GLN Chi-restraints excluded: chain f residue 203 LYS Chi-restraints excluded: chain f residue 250 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 628 optimal weight: 0.5980 chunk 641 optimal weight: 1.9990 chunk 552 optimal weight: 0.9990 chunk 120 optimal weight: 0.0370 chunk 655 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 422 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 505 optimal weight: 1.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 341 GLN A 576 GLN A 731 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 518 HIS B1068 GLN B1101 GLN B1145 GLN C 177 ASN E 30 GLN I 45 GLN L 26 ASN M 30 ASN a 9 GLN a 47 ASN a 230 ASN a 357 ASN b 956 GLN ** b 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 HIS d 970 ASN d 993 GLN d1056 ASN f 64 GLN f 78 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.181389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.149433 restraints weight = 71056.709| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.47 r_work: 0.3946 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 55931 Z= 0.225 Angle : 0.575 13.050 75997 Z= 0.304 Chirality : 0.044 0.241 8490 Planarity : 0.004 0.055 9523 Dihedral : 11.980 178.643 8307 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.36 % Allowed : 18.12 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.10), residues: 6568 helix: 1.25 (0.12), residues: 2037 sheet: 0.19 (0.13), residues: 1408 loop : -0.08 (0.11), residues: 3123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP f 174 HIS 0.005 0.001 HIS b 598 PHE 0.026 0.002 PHE M 57 TYR 0.018 0.001 TYR F 115 ARG 0.019 0.001 ARG f 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1429 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 1292 time to evaluate : 4.691 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 20 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7752 (ptm-80) REVERT: A 266 MET cc_start: 0.3809 (mmm) cc_final: 0.1971 (mmm) REVERT: A 418 TYR cc_start: 0.8638 (m-80) cc_final: 0.8359 (m-80) REVERT: A 421 ARG cc_start: 0.8461 (mtt180) cc_final: 0.8103 (mtt90) REVERT: A 561 MET cc_start: 0.8992 (mtt) cc_final: 0.8689 (mtt) REVERT: A 845 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 951 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: A 960 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7886 (ttm170) REVERT: A 1143 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8536 (mt) REVERT: A 1215 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 1221 MET cc_start: 0.7981 (mmm) cc_final: 0.7729 (tpt) REVERT: A 1228 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.6709 (mmm) REVERT: A 1233 GLU cc_start: 0.8004 (tp30) cc_final: 0.7781 (tp30) REVERT: A 1284 PHE cc_start: 0.8595 (t80) cc_final: 0.8383 (t80) REVERT: A 1289 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: A 1306 LYS cc_start: 0.8116 (tptp) cc_final: 0.7869 (tptp) REVERT: A 1422 GLN cc_start: 0.7654 (mt0) cc_final: 0.7356 (mt0) REVERT: A 1454 VAL cc_start: 0.8661 (m) cc_final: 0.8431 (t) REVERT: A 1478 GLU cc_start: 0.7924 (tp30) cc_final: 0.7467 (tp30) REVERT: B 381 GLU cc_start: 0.7822 (mp0) cc_final: 0.7588 (mp0) REVERT: B 497 LYS cc_start: 0.7829 (tptp) cc_final: 0.7544 (tptp) REVERT: B 508 MET cc_start: 0.8872 (mmt) cc_final: 0.7814 (mmt) REVERT: B 638 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7718 (ptt-90) REVERT: B 645 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: B 702 MET cc_start: 0.9166 (mmp) cc_final: 0.8892 (mmp) REVERT: B 744 MET cc_start: 0.8527 (mmt) cc_final: 0.7884 (mmt) REVERT: B 890 ARG cc_start: 0.6991 (ttp-110) cc_final: 0.6713 (ttp-110) REVERT: B 1054 MET cc_start: 0.8704 (mtm) cc_final: 0.8103 (mtm) REVERT: B 1071 ASN cc_start: 0.8270 (p0) cc_final: 0.8029 (p0) REVERT: B 1076 GLU cc_start: 0.7444 (tt0) cc_final: 0.7088 (tt0) REVERT: C 126 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7577 (mtp85) REVERT: F 80 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7835 (mmm) REVERT: H 45 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8511 (pp) REVERT: K 17 LYS cc_start: 0.8501 (mtmt) cc_final: 0.8064 (mtmt) REVERT: a 52 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7508 (pp20) REVERT: c 12 LEU cc_start: 0.8079 (mm) cc_final: 0.7687 (tp) REVERT: c 68 LEU cc_start: 0.8783 (mt) cc_final: 0.8099 (tm) REVERT: c 77 MET cc_start: 0.7829 (tmm) cc_final: 0.7456 (tmm) REVERT: c 110 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7254 (ttm170) REVERT: d 234 GLN cc_start: 0.8134 (tt0) cc_final: 0.7934 (mt0) REVERT: d 652 CYS cc_start: 0.2858 (OUTLIER) cc_final: 0.1431 (t) REVERT: d 693 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6718 (mp) REVERT: d 709 LYS cc_start: 0.7850 (pptt) cc_final: 0.7186 (pptt) REVERT: d 873 MET cc_start: 0.8390 (mtm) cc_final: 0.7963 (mtp) REVERT: d 1102 ARG cc_start: 0.7565 (mmm160) cc_final: 0.7320 (mmt180) REVERT: f 104 PHE cc_start: 0.8755 (m-80) cc_final: 0.8550 (m-80) REVERT: f 205 ARG cc_start: 0.7744 (mmt180) cc_final: 0.7183 (mmt180) REVERT: f 207 LEU cc_start: 0.8397 (tp) cc_final: 0.8191 (tt) outliers start: 137 outliers final: 84 residues processed: 1343 average time/residue: 1.6033 time to fit residues: 2636.0403 Evaluate side-chains 1377 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1281 time to evaluate : 4.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 174 LYS Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 296 LYS Chi-restraints excluded: chain a residue 348 GLU Chi-restraints excluded: chain b residue 747 LYS Chi-restraints excluded: chain b residue 752 MET Chi-restraints excluded: chain b residue 771 GLU Chi-restraints excluded: chain b residue 843 VAL Chi-restraints excluded: chain b residue 848 LEU Chi-restraints excluded: chain b residue 909 VAL Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 667 THR Chi-restraints excluded: chain c residue 674 ARG Chi-restraints excluded: chain d residue 16 ASN Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 70 LYS Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 430 VAL Chi-restraints excluded: chain d residue 437 MET Chi-restraints excluded: chain d residue 652 CYS Chi-restraints excluded: chain d residue 693 LEU Chi-restraints excluded: chain d residue 801 VAL Chi-restraints excluded: chain d residue 1041 THR Chi-restraints excluded: chain d residue 1053 ASP Chi-restraints excluded: chain d residue 1083 GLU Chi-restraints excluded: chain f residue 126 GLN Chi-restraints excluded: chain f residue 193 GLN Chi-restraints excluded: chain f residue 198 MET Chi-restraints excluded: chain f residue 203 LYS Chi-restraints excluded: chain f residue 250 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 224 optimal weight: 3.9990 chunk 620 optimal weight: 0.7980 chunk 290 optimal weight: 2.9990 chunk 360 optimal weight: 5.9990 chunk 413 optimal weight: 0.6980 chunk 333 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 541 optimal weight: 0.3980 chunk 297 optimal weight: 1.9990 chunk 358 optimal weight: 0.7980 chunk 477 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 288 ASN A 341 GLN A 731 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN B1101 GLN C 5 ASN C 177 ASN E 30 GLN H 44 ASN I 45 GLN L 26 ASN M 30 ASN a 9 GLN a 230 ASN a 343 GLN a 357 ASN b 618 HIS b 632 GLN b 956 GLN ** b 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 HIS d 970 ASN d 993 GLN f 236 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.181176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.148961 restraints weight = 71224.572| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.73 r_work: 0.3923 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 55931 Z= 0.216 Angle : 0.577 12.691 75997 Z= 0.305 Chirality : 0.044 0.243 8490 Planarity : 0.004 0.062 9523 Dihedral : 11.955 179.253 8307 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.06 % Allowed : 18.48 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.10), residues: 6568 helix: 1.23 (0.12), residues: 2059 sheet: 0.17 (0.13), residues: 1414 loop : -0.09 (0.11), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP f 174 HIS 0.004 0.001 HIS f 228 PHE 0.027 0.002 PHE M 57 TYR 0.063 0.001 TYR b1250 ARG 0.014 0.001 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1432 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1312 time to evaluate : 4.594 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: A 20 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7770 (ptm-80) REVERT: A 266 MET cc_start: 0.3743 (mmm) cc_final: 0.1987 (mmm) REVERT: A 418 TYR cc_start: 0.8657 (m-80) cc_final: 0.8388 (m-80) REVERT: A 421 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8109 (mtt90) REVERT: A 561 MET cc_start: 0.8978 (mtt) cc_final: 0.8679 (mtt) REVERT: A 769 MET cc_start: 0.8782 (mtm) cc_final: 0.8546 (mtp) REVERT: A 845 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7182 (mm-30) REVERT: A 951 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: A 960 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7934 (ttm170) REVERT: A 1143 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8515 (mt) REVERT: A 1215 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 1221 MET cc_start: 0.7997 (mmm) cc_final: 0.7769 (tpt) REVERT: A 1228 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.6699 (mmm) REVERT: A 1233 GLU cc_start: 0.8071 (tp30) cc_final: 0.7813 (tp30) REVERT: A 1284 PHE cc_start: 0.8601 (t80) cc_final: 0.8376 (t80) REVERT: A 1289 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: A 1306 LYS cc_start: 0.8186 (tptp) cc_final: 0.7938 (tptp) REVERT: A 1422 GLN cc_start: 0.7666 (mt0) cc_final: 0.7338 (mt0) REVERT: A 1454 VAL cc_start: 0.8613 (m) cc_final: 0.8390 (t) REVERT: A 1478 GLU cc_start: 0.7911 (tp30) cc_final: 0.7433 (tp30) REVERT: B 381 GLU cc_start: 0.7915 (mp0) cc_final: 0.7682 (mp0) REVERT: B 497 LYS cc_start: 0.7894 (tptp) cc_final: 0.7610 (tptp) REVERT: B 508 MET cc_start: 0.8876 (mmt) cc_final: 0.7819 (mmt) REVERT: B 645 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: B 702 MET cc_start: 0.9140 (mmp) cc_final: 0.8856 (mmp) REVERT: B 744 MET cc_start: 0.8557 (mmt) cc_final: 0.7907 (mmt) REVERT: B 890 ARG cc_start: 0.6997 (ttp-110) cc_final: 0.6706 (ttp-110) REVERT: B 1054 MET cc_start: 0.8701 (mtm) cc_final: 0.8092 (mtm) REVERT: B 1071 ASN cc_start: 0.8265 (p0) cc_final: 0.8019 (p0) REVERT: B 1076 GLU cc_start: 0.7490 (tt0) cc_final: 0.7135 (tt0) REVERT: C 126 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7658 (mtp85) REVERT: F 80 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.7884 (mmm) REVERT: H 45 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8531 (pp) REVERT: a 52 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: b 578 MET cc_start: 0.8007 (mtt) cc_final: 0.7650 (mtt) REVERT: c 1 MET cc_start: 0.5923 (tmm) cc_final: 0.5692 (tmm) REVERT: c 12 LEU cc_start: 0.8104 (mm) cc_final: 0.7696 (tp) REVERT: c 45 LEU cc_start: 0.8305 (tp) cc_final: 0.8022 (tp) REVERT: c 68 LEU cc_start: 0.8772 (mt) cc_final: 0.8107 (tm) REVERT: c 77 MET cc_start: 0.7944 (tmm) cc_final: 0.7567 (tmm) REVERT: d 652 CYS cc_start: 0.2722 (OUTLIER) cc_final: 0.1387 (t) REVERT: d 693 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6708 (mp) REVERT: d 709 LYS cc_start: 0.7878 (pptt) cc_final: 0.7231 (pptt) REVERT: d 873 MET cc_start: 0.8452 (mtm) cc_final: 0.8034 (mtp) REVERT: d 1102 ARG cc_start: 0.7673 (mmm160) cc_final: 0.7417 (mmt180) REVERT: f 205 ARG cc_start: 0.7904 (mmt180) cc_final: 0.7257 (mmt180) outliers start: 120 outliers final: 83 residues processed: 1358 average time/residue: 1.6510 time to fit residues: 2739.1914 Evaluate side-chains 1387 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1293 time to evaluate : 4.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 174 LYS Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 296 LYS Chi-restraints excluded: chain a residue 348 GLU Chi-restraints excluded: chain b residue 676 SER Chi-restraints excluded: chain b residue 692 ILE Chi-restraints excluded: chain b residue 747 LYS Chi-restraints excluded: chain b residue 752 MET Chi-restraints excluded: chain b residue 836 LYS Chi-restraints excluded: chain b residue 843 VAL Chi-restraints excluded: chain b residue 897 LEU Chi-restraints excluded: chain b residue 909 VAL Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 667 THR Chi-restraints excluded: chain d residue 16 ASN Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 430 VAL Chi-restraints excluded: chain d residue 437 MET Chi-restraints excluded: chain d residue 652 CYS Chi-restraints excluded: chain d residue 693 LEU Chi-restraints excluded: chain d residue 801 VAL Chi-restraints excluded: chain d residue 1041 THR Chi-restraints excluded: chain d residue 1053 ASP Chi-restraints excluded: chain d residue 1083 GLU Chi-restraints excluded: chain f residue 126 GLN Chi-restraints excluded: chain f residue 193 GLN Chi-restraints excluded: chain f residue 198 MET Chi-restraints excluded: chain f residue 203 LYS Chi-restraints excluded: chain f residue 250 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 470 optimal weight: 0.0070 chunk 334 optimal weight: 3.9990 chunk 541 optimal weight: 0.7980 chunk 429 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 250 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 284 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 341 GLN A 576 GLN A 731 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 518 HIS B1068 GLN C 5 ASN C 177 ASN E 71 GLN I 45 GLN L 26 ASN a 9 GLN a 230 ASN a 357 ASN b 956 GLN ** b 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 HIS d 759 GLN d 970 ASN d 993 GLN f 92 GLN f 236 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.181656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.149613 restraints weight = 71340.648| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.71 r_work: 0.3939 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 55931 Z= 0.186 Angle : 0.575 12.681 75997 Z= 0.303 Chirality : 0.044 0.202 8490 Planarity : 0.004 0.059 9523 Dihedral : 11.940 180.000 8307 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.72 % Allowed : 19.27 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.10), residues: 6568 helix: 1.27 (0.12), residues: 2059 sheet: 0.19 (0.13), residues: 1409 loop : -0.08 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP f 174 HIS 0.004 0.001 HIS f 228 PHE 0.026 0.001 PHE M 57 TYR 0.045 0.001 TYR b1250 ARG 0.015 0.001 ARG I 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1314 time to evaluate : 4.582 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: A 266 MET cc_start: 0.3741 (mmm) cc_final: 0.1950 (mmm) REVERT: A 317 MET cc_start: 0.7785 (ttp) cc_final: 0.7550 (ttt) REVERT: A 418 TYR cc_start: 0.8639 (m-80) cc_final: 0.8328 (m-80) REVERT: A 421 ARG cc_start: 0.8471 (mtt180) cc_final: 0.8126 (mtt90) REVERT: A 561 MET cc_start: 0.8993 (mtt) cc_final: 0.8702 (mtt) REVERT: A 769 MET cc_start: 0.8773 (mtm) cc_final: 0.8540 (mtp) REVERT: A 845 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7194 (mm-30) REVERT: A 951 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: A 960 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7923 (ttm170) REVERT: A 1143 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8491 (mt) REVERT: A 1215 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7418 (mt-10) REVERT: A 1221 MET cc_start: 0.7933 (mmm) cc_final: 0.7732 (tpt) REVERT: A 1228 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.6696 (mmm) REVERT: A 1233 GLU cc_start: 0.8082 (tp30) cc_final: 0.7841 (tp30) REVERT: A 1284 PHE cc_start: 0.8589 (t80) cc_final: 0.8380 (t80) REVERT: A 1289 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: A 1306 LYS cc_start: 0.8202 (tptp) cc_final: 0.7943 (tptp) REVERT: A 1422 GLN cc_start: 0.7650 (mt0) cc_final: 0.7327 (mt0) REVERT: A 1454 VAL cc_start: 0.8601 (m) cc_final: 0.8378 (t) REVERT: A 1478 GLU cc_start: 0.7953 (tp30) cc_final: 0.7460 (tp30) REVERT: B 381 GLU cc_start: 0.7924 (mp0) cc_final: 0.7684 (mp0) REVERT: B 497 LYS cc_start: 0.7863 (tptp) cc_final: 0.7575 (tptp) REVERT: B 508 MET cc_start: 0.8882 (mmt) cc_final: 0.7845 (mmt) REVERT: B 645 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: B 702 MET cc_start: 0.9120 (mmp) cc_final: 0.8857 (mmp) REVERT: B 744 MET cc_start: 0.8547 (mmt) cc_final: 0.7897 (mmt) REVERT: B 890 ARG cc_start: 0.7025 (ttp-110) cc_final: 0.6731 (ttp-110) REVERT: B 1054 MET cc_start: 0.8687 (mtm) cc_final: 0.8045 (mtm) REVERT: B 1071 ASN cc_start: 0.8270 (p0) cc_final: 0.8025 (p0) REVERT: C 126 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7613 (mtp85) REVERT: E 15 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8502 (ttmm) REVERT: F 80 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7867 (mmm) REVERT: H 45 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8497 (pp) REVERT: a 52 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7494 (pp20) REVERT: b 578 MET cc_start: 0.7890 (mtt) cc_final: 0.7533 (mtt) REVERT: c 1 MET cc_start: 0.5881 (tmm) cc_final: 0.5655 (tmm) REVERT: c 12 LEU cc_start: 0.8123 (mm) cc_final: 0.7717 (tp) REVERT: c 45 LEU cc_start: 0.8302 (tp) cc_final: 0.8018 (tp) REVERT: c 68 LEU cc_start: 0.8778 (mt) cc_final: 0.8124 (tm) REVERT: c 77 MET cc_start: 0.7930 (tmm) cc_final: 0.7565 (tmm) REVERT: c 110 ARG cc_start: 0.7768 (ttm170) cc_final: 0.7267 (ttm170) REVERT: d 652 CYS cc_start: 0.2685 (OUTLIER) cc_final: 0.1377 (t) REVERT: d 693 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6732 (mp) REVERT: d 709 LYS cc_start: 0.7887 (pptt) cc_final: 0.7303 (pptt) REVERT: d 873 MET cc_start: 0.8426 (mtm) cc_final: 0.8014 (mtp) REVERT: d 933 LEU cc_start: 0.8426 (mt) cc_final: 0.8183 (mt) REVERT: d 1102 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7427 (mmt180) REVERT: f 205 ARG cc_start: 0.7949 (mmt180) cc_final: 0.7309 (mmt180) REVERT: f 207 LEU cc_start: 0.8361 (tp) cc_final: 0.8155 (tt) REVERT: f 215 ARG cc_start: 0.7672 (ttm110) cc_final: 0.7294 (ttm-80) outliers start: 100 outliers final: 70 residues processed: 1350 average time/residue: 1.6103 time to fit residues: 2655.7473 Evaluate side-chains 1367 residues out of total 5856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 1287 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 174 LYS Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 296 LYS Chi-restraints excluded: chain a residue 348 GLU Chi-restraints excluded: chain b residue 676 SER Chi-restraints excluded: chain b residue 692 ILE Chi-restraints excluded: chain b residue 747 LYS Chi-restraints excluded: chain b residue 752 MET Chi-restraints excluded: chain b residue 836 LYS Chi-restraints excluded: chain b residue 843 VAL Chi-restraints excluded: chain b residue 897 LEU Chi-restraints excluded: chain b residue 909 VAL Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 667 THR Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 430 VAL Chi-restraints excluded: chain d residue 437 MET Chi-restraints excluded: chain d residue 652 CYS Chi-restraints excluded: chain d residue 693 LEU Chi-restraints excluded: chain d residue 801 VAL Chi-restraints excluded: chain d residue 1041 THR Chi-restraints excluded: chain d residue 1083 GLU Chi-restraints excluded: chain f residue 126 GLN Chi-restraints excluded: chain f residue 193 GLN Chi-restraints excluded: chain f residue 198 MET Chi-restraints excluded: chain f residue 203 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 414 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 470 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 608 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 510 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 250 optimal weight: 0.0670 chunk 196 optimal weight: 0.9980 chunk 630 optimal weight: 0.2980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 341 GLN A 576 GLN A 731 ASN A1417 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 518 HIS B1068 GLN B1101 GLN C 177 ASN E 132 GLN H 44 ASN I 45 GLN L 26 ASN a 9 GLN a 230 ASN a 283 ASN a 343 GLN a 357 ASN b 943 GLN b 956 GLN ** b 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 HIS d 790 ASN d 970 ASN d 993 GLN f 236 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.181847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.149838 restraints weight = 71580.641| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.71 r_work: 0.3940 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 55931 Z= 0.175 Angle : 0.565 12.516 75997 Z= 0.297 Chirality : 0.043 0.238 8490 Planarity : 0.004 0.066 9523 Dihedral : 11.932 179.295 8307 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.63 % Allowed : 19.58 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.10), residues: 6568 helix: 1.38 (0.12), residues: 2044 sheet: 0.19 (0.13), residues: 1408 loop : -0.06 (0.11), residues: 3116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP f 174 HIS 0.004 0.001 HIS f 228 PHE 0.028 0.001 PHE M 57 TYR 0.049 0.001 TYR b1250 ARG 0.015 0.000 ARG I 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 86583.77 seconds wall clock time: 1466 minutes 50.41 seconds (88010.41 seconds total)