Starting phenix.real_space_refine on Sun Feb 8 09:29:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oti_70833/02_2026/9oti_70833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oti_70833/02_2026/9oti_70833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oti_70833/02_2026/9oti_70833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oti_70833/02_2026/9oti_70833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oti_70833/02_2026/9oti_70833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oti_70833/02_2026/9oti_70833.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.020 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 29 6.06 5 S 288 5.16 5 C 27610 2.51 5 N 7653 2.21 5 O 7745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43325 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3232 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 12, 'TRANS': 421} Chain breaks: 6 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 7, 'GLN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 151 Chain: "B" Number of atoms: 4768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 4768 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 231} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 664} Chain breaks: 13 Unresolved non-hydrogen bonds: 812 Unresolved non-hydrogen angles: 1019 Unresolved non-hydrogen dihedrals: 664 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ASP:plan': 25, 'ARG:plan': 19, 'GLU:plan': 26, 'HIS:plan': 6, 'ASN:plan1': 13, 'TYR:plan': 6, 'PHE:plan': 4, 'GLN:plan1': 13, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 488 Chain: "C" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1668 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 4 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 7, 'ARG:plan': 10, 'GLN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 133 Chain: "D" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1657 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain breaks: 3 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 4, 'ARG:plan': 8, 'GLN:plan1': 7, 'ASP:plan': 8, 'GLU:plan': 12} Unresolved non-hydrogen planarities: 173 Chain: "E" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2017 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 5 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 8, 'ASP:plan': 13, 'HIS:plan': 3, 'GLU:plan': 9, 'ASN:plan1': 7, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 163 Chain: "F" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1464 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain breaks: 9 Unresolved non-hydrogen bonds: 549 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'ARG:plan': 13, 'HIS:plan': 7, 'ASP:plan': 16, 'GLN:plan1': 5, 'TRP:plan': 3, 'GLU:plan': 7, 'PHE:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 290 Chain: "G" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2062 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 4 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 7, 'HIS:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "H" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 1989 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 7, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 7, 'GLN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "L" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3498 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 6 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "M" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1870 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 236} Chain breaks: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 37 Chain: "N" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1881 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 5, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "O" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2352 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 3 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "P" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 1660 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain breaks: 5 Unresolved non-hydrogen bonds: 643 Unresolved non-hydrogen angles: 817 Unresolved non-hydrogen dihedrals: 532 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'PHE:plan': 5, 'ARG:plan': 14, 'ASP:plan': 20, 'HIS:plan': 8, 'GLN:plan1': 4, 'TRP:plan': 4, 'GLU:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 334 Chain: "Q" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2343 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2171 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "T" Number of atoms: 4771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 4771 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 256} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 672} Chain breaks: 10 Unresolved non-hydrogen bonds: 862 Unresolved non-hydrogen angles: 1078 Unresolved non-hydrogen dihedrals: 693 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'ASP:plan': 27, 'HIS:plan': 6, 'ARG:plan': 18, 'GLU:plan': 23, 'ASN:plan1': 18, 'TYR:plan': 6, 'PHE:plan': 5, 'GLN:plan1': 12, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 476 Chain: "U" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1946 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 4, 'GLN:plan1': 6, 'HIS:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "V" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1947 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain breaks: 6 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 6, 'GLN:plan1': 5, 'HIS:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 152 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2608 SG CYS A 737 47.507 168.064 201.312 1.00108.21 S ATOM 2633 SG CYS A 740 47.237 171.718 200.364 1.00111.09 S ATOM 2698 SG CYS A 775 50.619 170.062 200.246 1.00106.25 S ATOM 2715 SG CYS A 778 48.934 170.675 203.632 1.00109.96 S ATOM 2764 SG CYS A 785 53.205 152.351 195.229 1.00 90.34 S ATOM 2783 SG CYS A 788 56.490 151.985 197.089 1.00 92.98 S ATOM 2955 SG CYS A 827 41.594 153.464 186.925 1.00 92.98 S ATOM 2979 SG CYS A 830 40.776 152.399 190.499 1.00 98.59 S ATOM 3177 SG CYS A 856 39.276 150.609 187.424 1.00103.54 S ATOM 3192 SG CYS A 858 43.002 150.257 188.189 1.00100.74 S ATOM 2979 SG CYS A 830 40.776 152.399 190.499 1.00 98.59 S ATOM 3133 SG CYS A 849 42.969 149.823 192.334 1.00101.29 S ATOM 3164 SG CYS A 854 39.209 149.608 192.728 1.00108.18 S ATOM 7624 SG CYS B 785 52.884 75.379 207.108 1.00102.61 S ATOM 7643 SG CYS B 788 49.373 74.554 208.533 1.00 98.15 S ATOM 7747 SG CYS B 827 65.867 77.312 203.782 1.00102.46 S ATOM 7766 SG CYS B 830 64.813 79.656 206.532 1.00109.24 S ATOM 7958 SG CYS B 856 66.576 81.091 203.451 1.00114.13 S ATOM 7969 SG CYS B 858 63.036 79.723 203.169 1.00107.91 S ATOM 7766 SG CYS B 830 64.813 79.656 206.532 1.00109.24 S ATOM 7914 SG CYS B 849 61.288 81.200 206.338 1.00106.72 S ATOM 7945 SG CYS B 854 64.214 83.308 207.605 1.00109.40 S ATOM 7624 SG CYS B 785 52.884 75.379 207.108 1.00102.61 S ATOM 9191 SG CYS C 719 40.123 170.913 183.593 1.00114.52 S ATOM 9208 SG CYS C 722 38.061 172.765 186.155 1.00117.64 S ATOM 9278 SG CYS C 733 36.312 170.427 183.816 1.00122.81 S ATOM 9294 SG CYS C 736 37.699 173.700 182.498 1.00125.58 S ATOM 9335 SG CYS C 743 48.008 158.925 175.632 1.00 75.86 S ATOM 9353 SG CYS C 746 46.848 157.356 172.318 1.00 69.57 S ATOM 9442 SG CYS C 757 57.252 165.654 185.244 1.00 89.44 S ATOM 9461 SG CYS C 760 55.687 167.803 182.517 1.00 93.21 S ATOM 9646 SG CYS C 787 58.717 165.718 181.728 1.00 94.48 S ATOM 9461 SG CYS C 760 55.687 167.803 182.517 1.00 93.21 S ATOM 9599 SG CYS C 779 55.456 166.812 178.808 1.00 81.75 S ATOM 9621 SG CYS C 783 56.443 170.389 179.754 1.00 87.58 S ATOM 11006 SG CYS D 924 66.826 67.002 193.846 1.00 88.85 S ATOM 11025 SG CYS D 927 68.356 69.057 190.996 1.00 87.58 S ATOM 11092 SG CYS D 938 60.122 59.122 203.157 1.00108.21 S ATOM 11110 SG CYS D 941 63.087 57.652 201.368 1.00113.93 S ATOM 11273 SG CYS D 966 59.838 55.663 201.543 1.00113.07 S ATOM 11289 SG CYS D 968 59.985 58.857 199.421 1.00113.00 S ATOM 11110 SG CYS D 941 63.087 57.652 201.368 1.00113.93 S ATOM 11241 SG CYS D 960 63.211 58.068 197.541 1.00 94.00 S ATOM 11263 SG CYS D 964 64.178 54.708 199.052 1.00107.27 S ATOM 21685 SG CYS L 737 50.749 49.408 53.859 1.00 81.61 S ATOM 21710 SG CYS L 740 49.889 45.849 54.925 1.00 85.27 S ATOM 21789 SG CYS L 775 53.431 47.052 55.320 1.00 86.08 S ATOM 21806 SG CYS L 778 51.951 46.498 51.816 1.00 92.08 S ATOM 21865 SG CYS L 785 56.507 64.662 60.770 1.00 54.60 S ATOM 21884 SG CYS L 788 59.703 64.609 58.634 1.00 53.11 S ATOM 22078 SG CYS L 827 44.126 64.273 67.465 1.00 55.83 S ATOM 22102 SG CYS L 830 43.891 65.321 63.839 1.00 56.94 S ATOM 22300 SG CYS L 856 42.182 67.332 66.593 1.00 58.82 S ATOM 22315 SG CYS L 858 46.038 67.290 66.382 1.00 55.07 S ATOM 22102 SG CYS L 830 43.891 65.321 63.839 1.00 56.94 S ATOM 22256 SG CYS L 849 46.284 67.778 62.096 1.00 52.09 S ATOM 22287 SG CYS L 854 42.570 67.893 61.183 1.00 59.68 S ATOM 23693 SG CYS M 719 41.156 46.656 70.427 1.00 79.66 S ATOM 23715 SG CYS M 722 39.543 45.150 67.282 1.00 87.05 S ATOM 23798 SG CYS M 733 37.524 47.379 69.468 1.00 96.89 S ATOM 23817 SG CYS M 736 38.364 44.004 70.768 1.00102.72 S ATOM 23869 SG CYS M 743 50.076 57.459 78.820 1.00 37.90 S ATOM 23887 SG CYS M 746 47.647 58.858 81.501 1.00 37.54 S ATOM 23980 SG CYS M 757 58.560 50.580 70.575 1.00 51.56 S ATOM 23999 SG CYS M 760 56.623 48.489 73.138 1.00 48.00 S ATOM 24198 SG CYS M 787 59.653 50.374 74.218 1.00 57.47 S ATOM 23999 SG CYS M 760 56.623 48.489 73.138 1.00 48.00 S ATOM 24148 SG CYS M 779 56.213 49.198 76.832 1.00 38.85 S ATOM 24170 SG CYS M 783 56.869 45.628 75.665 1.00 46.27 S ATOM 25758 SG CYS N 924 75.736 149.290 63.910 1.00 57.16 S ATOM 25777 SG CYS N 927 77.446 147.030 66.486 1.00 52.10 S ATOM 25852 SG CYS N 938 70.355 157.524 54.357 1.00 82.90 S ATOM 25873 SG CYS N 941 73.400 158.792 56.240 1.00 86.21 S ATOM 26051 SG CYS N 966 70.355 161.103 55.631 1.00 81.14 S ATOM 26067 SG CYS N 968 70.166 158.124 58.046 1.00 79.22 S ATOM 25873 SG CYS N 941 73.400 158.792 56.240 1.00 86.21 S ATOM 26017 SG CYS N 960 73.604 158.119 60.073 1.00 66.93 S ATOM 26041 SG CYS N 964 74.297 161.639 58.776 1.00 75.03 S ATOM 38986 SG CYS T 785 62.554 141.663 49.557 1.00 57.58 S ATOM 39005 SG CYS T 788 59.193 142.804 48.076 1.00 54.01 S ATOM 39132 SG CYS T 827 75.051 139.171 53.992 1.00 74.77 S ATOM 39156 SG CYS T 830 73.954 136.902 51.210 1.00 75.65 S ATOM 39348 SG CYS T 856 75.203 135.357 54.425 1.00 76.52 S ATOM 39363 SG CYS T 858 71.885 137.210 54.475 1.00 76.53 S ATOM 39156 SG CYS T 830 73.954 136.902 51.210 1.00 75.65 S ATOM 39304 SG CYS T 849 70.415 135.451 50.786 1.00 62.02 S ATOM 39335 SG CYS T 854 73.452 133.347 49.743 1.00 68.72 S Time building chain proxies: 10.31, per 1000 atoms: 0.24 Number of scatterers: 43325 At special positions: 0 Unit cell: (159.6, 215.25, 256.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 29 29.99 S 288 16.00 O 7745 8.00 N 7653 7.00 C 27610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 740 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 737 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 778 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 775 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 838 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 835 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 788 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 785 " pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 827 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 858 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 856 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 830 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" ND1 HIS A 832 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 849 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 854 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 830 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" ND1 HIS B 838 " pdb="ZN ZN B 901 " - pdb=" ND1 HIS B 835 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 788 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 785 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 858 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 827 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 830 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 856 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" ND1 HIS B 832 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 849 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 854 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 830 " pdb=" ZN B 904 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 785 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 722 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 733 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 736 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 719 " pdb=" ZN C1002 " pdb="ZN ZN C1002 " - pdb=" ND1 HIS C 768 " pdb="ZN ZN C1002 " - pdb=" ND1 HIS C 765 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 746 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 743 " pdb=" ZN C1003 " pdb="ZN ZN C1003 " - pdb=" NE2 HIS C 785 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 787 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 757 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 760 " pdb=" ZN C1004 " pdb="ZN ZN C1004 " - pdb=" ND1 HIS C 762 " pdb="ZN ZN C1004 " - pdb=" SG CYS C 779 " pdb="ZN ZN C1004 " - pdb=" SG CYS C 783 " pdb="ZN ZN C1004 " - pdb=" SG CYS C 760 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" ND1 HIS D 949 " pdb="ZN ZN D1001 " - pdb=" ND1 HIS D 946 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 927 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 924 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 938 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 941 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 968 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 966 " pdb=" ZN D1003 " pdb="ZN ZN D1003 " - pdb=" ND1 HIS D 943 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 960 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 964 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 941 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 740 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 778 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 737 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 775 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" ND1 HIS L 838 " pdb="ZN ZN L1002 " - pdb=" ND1 HIS L 835 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 788 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 785 " pdb=" ZN L1003 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 827 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 856 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 830 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 858 " pdb=" ZN L1004 " pdb="ZN ZN L1004 " - pdb=" ND1 HIS L 832 " pdb="ZN ZN L1004 " - pdb=" SG CYS L 849 " pdb="ZN ZN L1004 " - pdb=" SG CYS L 854 " pdb="ZN ZN L1004 " - pdb=" SG CYS L 830 " pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 733 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 722 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 736 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 719 " pdb=" ZN M1002 " pdb="ZN ZN M1002 " - pdb=" ND1 HIS M 765 " pdb="ZN ZN M1002 " - pdb=" ND1 HIS M 768 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 746 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 743 " pdb=" ZN M1003 " pdb="ZN ZN M1003 " - pdb=" ND1 HIS M 785 " pdb="ZN ZN M1003 " - pdb=" SG CYS M 787 " pdb="ZN ZN M1003 " - pdb=" SG CYS M 760 " pdb="ZN ZN M1003 " - pdb=" SG CYS M 757 " pdb=" ZN M1004 " pdb="ZN ZN M1004 " - pdb=" ND1 HIS M 762 " pdb="ZN ZN M1004 " - pdb=" SG CYS M 779 " pdb="ZN ZN M1004 " - pdb=" SG CYS M 760 " pdb="ZN ZN M1004 " - pdb=" SG CYS M 783 " pdb=" ZN N1001 " pdb="ZN ZN N1001 " - pdb=" ND1 HIS N 946 " pdb="ZN ZN N1001 " - pdb=" ND1 HIS N 949 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 927 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 924 " pdb=" ZN N1002 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 968 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 938 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 941 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 966 " pdb=" ZN N1003 " pdb="ZN ZN N1003 " - pdb=" ND1 HIS N 943 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 960 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 964 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 941 " pdb=" ZN T 901 " pdb="ZN ZN T 901 " - pdb=" ND1 HIS T 835 " pdb="ZN ZN T 901 " - pdb=" ND1 HIS T 838 " pdb="ZN ZN T 901 " - pdb=" SG CYS T 788 " pdb="ZN ZN T 901 " - pdb=" SG CYS T 785 " pdb=" ZN T 902 " pdb="ZN ZN T 902 " - pdb=" SG CYS T 827 " pdb="ZN ZN T 902 " - pdb=" SG CYS T 830 " pdb="ZN ZN T 902 " - pdb=" SG CYS T 856 " pdb="ZN ZN T 902 " - pdb=" SG CYS T 858 " pdb=" ZN T 903 " pdb="ZN ZN T 903 " - pdb=" ND1 HIS T 832 " pdb="ZN ZN T 903 " - pdb=" SG CYS T 849 " pdb="ZN ZN T 903 " - pdb=" SG CYS T 854 " pdb="ZN ZN T 903 " - pdb=" SG CYS T 830 " Number of angles added : 106 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11478 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 86 sheets defined 31.2% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 420 through 440 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 454 through 462 removed outlier: 3.987A pdb=" N SER A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 498 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 533 through 547 Processing helix chain 'A' and resid 553 through 562 removed outlier: 3.550A pdb=" N ALA A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.728A pdb=" N GLU A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.785A pdb=" N LEU A 583 " --> pdb=" O ARG A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 585 through 597 Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 612 through 624 Processing helix chain 'A' and resid 625 through 644 removed outlier: 4.273A pdb=" N ARG A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 655 through 670 Processing helix chain 'A' and resid 671 through 680 removed outlier: 3.631A pdb=" N ALA A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 690 Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.685A pdb=" N GLN A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 724 Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 835 through 846 Processing helix chain 'A' and resid 857 through 863 removed outlier: 3.910A pdb=" N ASP A 862 " --> pdb=" O CYS A 858 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 863 " --> pdb=" O MET A 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.837A pdb=" N ARG B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 421 through 438 Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 454 through 460 removed outlier: 4.261A pdb=" N SER B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 520 through 531 removed outlier: 3.518A pdb=" N ALA B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 547 Processing helix chain 'B' and resid 553 through 562 Processing helix chain 'B' and resid 570 through 580 removed outlier: 3.547A pdb=" N SER B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 585 through 597 Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.696A pdb=" N TYR B 607 " --> pdb=" O ASP B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 624 removed outlier: 3.531A pdb=" N LYS B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 644 removed outlier: 3.581A pdb=" N ARG B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 653 Processing helix chain 'B' and resid 655 through 669 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.500A pdb=" N ALA B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 689 Processing helix chain 'B' and resid 690 through 707 removed outlier: 3.517A pdb=" N ALA B 706 " --> pdb=" O ASN B 702 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP B 707 " --> pdb=" O LEU B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 724 Processing helix chain 'B' and resid 725 through 728 removed outlier: 3.619A pdb=" N LYS B 728 " --> pdb=" O PRO B 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 725 through 728' Processing helix chain 'B' and resid 819 through 823 removed outlier: 3.543A pdb=" N ASN B 822 " --> pdb=" O GLN B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 846 removed outlier: 4.085A pdb=" N ASP B 845 " --> pdb=" O SER B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 863 removed outlier: 4.202A pdb=" N ASP B 862 " --> pdb=" O CYS B 858 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR B 863 " --> pdb=" O MET B 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 418 Processing helix chain 'C' and resid 425 through 441 Processing helix chain 'C' and resid 442 through 457 Processing helix chain 'C' and resid 633 through 647 Processing helix chain 'C' and resid 649 through 661 removed outlier: 4.246A pdb=" N ALA C 653 " --> pdb=" O ASP C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 666 removed outlier: 4.174A pdb=" N LYS C 666 " --> pdb=" O GLU C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 687 Processing helix chain 'C' and resid 689 through 700 Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 708 through 710 No H-bonds generated for 'chain 'C' and resid 708 through 710' Processing helix chain 'C' and resid 766 through 774 Processing helix chain 'D' and resid 653 through 656 Processing helix chain 'D' and resid 659 through 666 Processing helix chain 'D' and resid 672 through 688 removed outlier: 3.687A pdb=" N THR D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 703 Processing helix chain 'D' and resid 704 through 708 Processing helix chain 'D' and resid 725 through 739 Processing helix chain 'D' and resid 741 through 756 removed outlier: 4.007A pdb=" N GLN D 755 " --> pdb=" O VAL D 751 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER D 756 " --> pdb=" O PHE D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 848 Processing helix chain 'D' and resid 852 through 854 No H-bonds generated for 'chain 'D' and resid 852 through 854' Processing helix chain 'D' and resid 855 through 874 removed outlier: 3.528A pdb=" N PHE D 859 " --> pdb=" O ASN D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 884 Processing helix chain 'D' and resid 947 through 955 Processing helix chain 'D' and resid 967 through 973 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.605A pdb=" N MET E 126 " --> pdb=" O PRO E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 123 through 127 Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'L' and resid 389 through 400 Processing helix chain 'L' and resid 408 through 410 No H-bonds generated for 'chain 'L' and resid 408 through 410' Processing helix chain 'L' and resid 411 through 416 Processing helix chain 'L' and resid 420 through 443 Processing helix chain 'L' and resid 451 through 453 No H-bonds generated for 'chain 'L' and resid 451 through 453' Processing helix chain 'L' and resid 454 through 462 removed outlier: 4.155A pdb=" N SER L 458 " --> pdb=" O ALA L 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER L 462 " --> pdb=" O SER L 458 " (cutoff:3.500A) Processing helix chain 'L' and resid 487 through 498 Processing helix chain 'L' and resid 508 through 519 Processing helix chain 'L' and resid 520 through 531 Processing helix chain 'L' and resid 533 through 547 Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 570 through 580 Processing helix chain 'L' and resid 581 through 583 No H-bonds generated for 'chain 'L' and resid 581 through 583' Processing helix chain 'L' and resid 585 through 597 removed outlier: 3.603A pdb=" N LEU L 595 " --> pdb=" O MET L 591 " (cutoff:3.500A) Processing helix chain 'L' and resid 602 through 607 Processing helix chain 'L' and resid 612 through 624 Processing helix chain 'L' and resid 625 through 644 removed outlier: 4.215A pdb=" N ARG L 631 " --> pdb=" O THR L 627 " (cutoff:3.500A) Processing helix chain 'L' and resid 645 through 647 No H-bonds generated for 'chain 'L' and resid 645 through 647' Processing helix chain 'L' and resid 648 through 653 Processing helix chain 'L' and resid 655 through 670 Processing helix chain 'L' and resid 671 through 680 removed outlier: 3.584A pdb=" N ALA L 675 " --> pdb=" O ASP L 671 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU L 680 " --> pdb=" O SER L 676 " (cutoff:3.500A) Processing helix chain 'L' and resid 684 through 689 Processing helix chain 'L' and resid 690 through 707 Processing helix chain 'L' and resid 709 through 724 Processing helix chain 'L' and resid 819 through 822 Processing helix chain 'L' and resid 836 through 846 Processing helix chain 'L' and resid 857 through 863 removed outlier: 4.070A pdb=" N ASP L 862 " --> pdb=" O CYS L 858 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR L 863 " --> pdb=" O MET L 859 " (cutoff:3.500A) Processing helix chain 'M' and resid 409 through 419 Processing helix chain 'M' and resid 425 through 441 Processing helix chain 'M' and resid 442 through 457 Processing helix chain 'M' and resid 633 through 647 removed outlier: 3.641A pdb=" N GLN M 647 " --> pdb=" O PHE M 643 " (cutoff:3.500A) Processing helix chain 'M' and resid 649 through 661 removed outlier: 3.571A pdb=" N ALA M 653 " --> pdb=" O ASP M 649 " (cutoff:3.500A) Processing helix chain 'M' and resid 661 through 666 removed outlier: 4.044A pdb=" N LYS M 666 " --> pdb=" O GLU M 662 " (cutoff:3.500A) Processing helix chain 'M' and resid 669 through 687 Processing helix chain 'M' and resid 689 through 700 Processing helix chain 'M' and resid 702 through 707 Processing helix chain 'M' and resid 766 through 776 Processing helix chain 'N' and resid 659 through 666 Processing helix chain 'N' and resid 673 through 688 Processing helix chain 'N' and resid 689 through 703 Processing helix chain 'N' and resid 704 through 708 removed outlier: 3.577A pdb=" N GLY N 708 " --> pdb=" O LEU N 705 " (cutoff:3.500A) Processing helix chain 'N' and resid 725 through 739 Processing helix chain 'N' and resid 741 through 755 removed outlier: 3.660A pdb=" N GLU N 753 " --> pdb=" O CYS N 749 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN N 755 " --> pdb=" O VAL N 751 " (cutoff:3.500A) Processing helix chain 'N' and resid 838 through 848 Processing helix chain 'N' and resid 852 through 854 No H-bonds generated for 'chain 'N' and resid 852 through 854' Processing helix chain 'N' and resid 855 through 874 Processing helix chain 'N' and resid 875 through 884 Processing helix chain 'N' and resid 947 through 955 removed outlier: 3.631A pdb=" N ARG N 955 " --> pdb=" O MET N 951 " (cutoff:3.500A) Processing helix chain 'N' and resid 967 through 973 Processing helix chain 'O' and resid 67 through 71 Processing helix chain 'O' and resid 123 through 127 Processing helix chain 'P' and resid 67 through 71 Processing helix chain 'P' and resid 123 through 127 Processing helix chain 'Q' and resid 67 through 71 Processing helix chain 'Q' and resid 123 through 127 Processing helix chain 'R' and resid 43 through 46 Processing helix chain 'R' and resid 67 through 71 Processing helix chain 'R' and resid 113 through 117 Processing helix chain 'T' and resid 254 through 256 No H-bonds generated for 'chain 'T' and resid 254 through 256' Processing helix chain 'T' and resid 389 through 400 removed outlier: 3.641A pdb=" N ARG T 395 " --> pdb=" O ALA T 391 " (cutoff:3.500A) Processing helix chain 'T' and resid 408 through 410 No H-bonds generated for 'chain 'T' and resid 408 through 410' Processing helix chain 'T' and resid 411 through 417 Processing helix chain 'T' and resid 420 through 441 removed outlier: 3.602A pdb=" N TYR T 436 " --> pdb=" O PHE T 432 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR T 437 " --> pdb=" O MET T 433 " (cutoff:3.500A) Processing helix chain 'T' and resid 451 through 454 Processing helix chain 'T' and resid 455 through 460 Processing helix chain 'T' and resid 487 through 498 Processing helix chain 'T' and resid 508 through 519 Processing helix chain 'T' and resid 520 through 531 Processing helix chain 'T' and resid 533 through 545 Processing helix chain 'T' and resid 553 through 562 Processing helix chain 'T' and resid 570 through 580 removed outlier: 4.142A pdb=" N THR T 578 " --> pdb=" O GLU T 574 " (cutoff:3.500A) Processing helix chain 'T' and resid 581 through 583 No H-bonds generated for 'chain 'T' and resid 581 through 583' Processing helix chain 'T' and resid 585 through 597 Processing helix chain 'T' and resid 602 through 607 removed outlier: 3.508A pdb=" N LEU T 606 " --> pdb=" O TYR T 602 " (cutoff:3.500A) Processing helix chain 'T' and resid 612 through 624 Processing helix chain 'T' and resid 625 through 644 removed outlier: 3.566A pdb=" N ASN T 630 " --> pdb=" O ASP T 626 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY T 644 " --> pdb=" O MET T 640 " (cutoff:3.500A) Processing helix chain 'T' and resid 645 through 647 No H-bonds generated for 'chain 'T' and resid 645 through 647' Processing helix chain 'T' and resid 648 through 653 Processing helix chain 'T' and resid 655 through 670 Processing helix chain 'T' and resid 671 through 679 removed outlier: 3.850A pdb=" N ALA T 675 " --> pdb=" O ASP T 671 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET T 679 " --> pdb=" O ALA T 675 " (cutoff:3.500A) Processing helix chain 'T' and resid 684 through 689 Processing helix chain 'T' and resid 690 through 707 removed outlier: 3.610A pdb=" N TRP T 707 " --> pdb=" O LEU T 703 " (cutoff:3.500A) Processing helix chain 'T' and resid 709 through 724 Processing helix chain 'T' and resid 817 through 823 removed outlier: 3.681A pdb=" N PHE T 820 " --> pdb=" O LEU T 817 " (cutoff:3.500A) Processing helix chain 'T' and resid 835 through 846 removed outlier: 4.141A pdb=" N ASP T 845 " --> pdb=" O SER T 841 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 22 removed outlier: 4.568A pdb=" N TRP U 21 " --> pdb=" O PRO U 18 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU U 22 " --> pdb=" O GLY U 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 18 through 22' Processing helix chain 'U' and resid 23 through 33 Processing helix chain 'U' and resid 34 through 37 Processing helix chain 'U' and resid 57 through 61 removed outlier: 3.501A pdb=" N LYS U 61 " --> pdb=" O GLU U 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 57 through 61' Processing helix chain 'U' and resid 101 through 108 Processing helix chain 'U' and resid 129 through 138 Processing helix chain 'U' and resid 197 through 207 Processing helix chain 'U' and resid 243 through 247 removed outlier: 3.818A pdb=" N LYS U 247 " --> pdb=" O ALA U 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 243 through 247' Processing helix chain 'U' and resid 279 through 291 removed outlier: 4.587A pdb=" N ILE U 284 " --> pdb=" O ILE U 280 " (cutoff:3.500A) Proline residue: U 287 - end of helix Processing helix chain 'U' and resid 312 through 320 Processing helix chain 'V' and resid 17 through 21 removed outlier: 4.279A pdb=" N TRP V 21 " --> pdb=" O PRO V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 23 through 33 Processing helix chain 'V' and resid 34 through 37 Processing helix chain 'V' and resid 56 through 61 removed outlier: 3.502A pdb=" N LYS V 61 " --> pdb=" O GLU V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 108 removed outlier: 3.640A pdb=" N LEU V 105 " --> pdb=" O VAL V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 129 through 138 Processing helix chain 'V' and resid 190 through 196 Proline residue: V 195 - end of helix Processing helix chain 'V' and resid 197 through 207 Processing helix chain 'V' and resid 243 through 247 removed outlier: 3.523A pdb=" N LYS V 247 " --> pdb=" O ALA V 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 243 through 247' Processing helix chain 'V' and resid 281 through 292 Proline residue: V 287 - end of helix Processing helix chain 'V' and resid 312 through 322 removed outlier: 3.504A pdb=" N ARG V 322 " --> pdb=" O GLU V 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 370 removed outlier: 3.740A pdb=" N HIS A 373 " --> pdb=" O CYS A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 734 through 736 removed outlier: 4.512A pdb=" N HIS C 716 " --> pdb=" O SER A 736 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 724 " --> pdb=" O CYS C 719 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.553A pdb=" N TRP A 826 " --> pdb=" O PHE C 754 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 10 removed outlier: 3.999A pdb=" N SER B 26 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 25 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE B 56 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 27 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 65 Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.611A pdb=" N THR B 118 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N SER B 141 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE B 140 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN B 183 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 203 Processing sheet with id=AA8, first strand: chain 'B' and resid 228 through 232 removed outlier: 3.678A pdb=" N GLN B 228 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL B 230 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 241 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL B 232 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG B 239 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 270 through 274 removed outlier: 4.069A pdb=" N LYS B 272 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 283 " --> pdb=" O TYR B 296 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 296 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 327 through 330 removed outlier: 3.621A pdb=" N SER B 327 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 339 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 367 through 370 removed outlier: 3.699A pdb=" N LEU B 374 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG F 5 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 344 through 345 Processing sheet with id=AB4, first strand: chain 'D' and resid 541 through 545 Processing sheet with id=AB5, first strand: chain 'D' and resid 935 through 937 Processing sheet with id=AB6, first strand: chain 'E' and resid 15 through 20 removed outlier: 4.040A pdb=" N ASP E 17 " --> pdb=" O CYS E 30 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL E 36 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL E 38 " --> pdb=" O THR E 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 60 through 65 removed outlier: 4.143A pdb=" N ARG E 62 " --> pdb=" O CYS E 77 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA E 83 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR E 108 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL E 85 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 116 through 121 removed outlier: 6.896A pdb=" N CYS E 133 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL E 119 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA E 131 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE E 121 " --> pdb=" O MET E 129 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N MET E 129 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS E 157 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU E 143 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU E 155 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 168 through 170 removed outlier: 7.111A pdb=" N VAL E 197 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR E 214 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE E 199 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN E 203 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 224 through 227 removed outlier: 3.960A pdb=" N ASP E 224 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 272 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR E 249 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE E 270 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LYS E 251 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE E 268 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 281 through 286 removed outlier: 6.485A pdb=" N VAL E 302 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE E 318 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU E 304 " --> pdb=" O THR E 316 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 15 through 20 removed outlier: 6.555A pdb=" N CYS F 30 " --> pdb=" O HIS F 16 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL F 18 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA F 28 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER F 35 " --> pdb=" O SER F 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 62 through 65 removed outlier: 3.673A pdb=" N ARG F 62 " --> pdb=" O CYS F 77 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL F 85 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR F 107 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 120 through 121 removed outlier: 5.932A pdb=" N VAL F 139 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU F 158 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE F 141 " --> pdb=" O GLN F 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 167 through 170 removed outlier: 3.588A pdb=" N LYS F 208 " --> pdb=" O ASN F 203 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 225 through 227 removed outlier: 3.572A pdb=" N ARG F 246 " --> pdb=" O ILE F 240 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 285 through 286 removed outlier: 3.589A pdb=" N ALA F 294 " --> pdb=" O SER F 285 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL F 302 " --> pdb=" O ILE F 318 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE F 318 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU F 304 " --> pdb=" O THR F 316 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 17 through 20 removed outlier: 3.696A pdb=" N TRP G 53 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA G 51 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP G 40 " --> pdb=" O CYS G 49 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N CYS G 49 " --> pdb=" O ASP G 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 60 through 65 removed outlier: 3.642A pdb=" N ARG G 62 " --> pdb=" O CYS G 77 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA G 83 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR G 108 " --> pdb=" O ALA G 83 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL G 85 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 116 through 121 removed outlier: 6.845A pdb=" N CYS G 133 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL G 119 " --> pdb=" O ALA G 131 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA G 131 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE G 121 " --> pdb=" O MET G 129 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET G 129 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS G 157 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLU G 143 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU G 155 " --> pdb=" O GLU G 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 165 through 170 removed outlier: 3.533A pdb=" N ALA G 183 " --> pdb=" O SER G 169 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL G 197 " --> pdb=" O THR G 214 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N THR G 214 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE G 199 " --> pdb=" O ALA G 212 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN G 203 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS G 208 " --> pdb=" O ASN G 203 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 224 through 227 removed outlier: 4.036A pdb=" N ASP G 224 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS G 251 " --> pdb=" O GLU G 267 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 224 through 227 removed outlier: 4.036A pdb=" N ASP G 224 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL G 245 " --> pdb=" O GLN G 273 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN G 273 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE G 247 " --> pdb=" O VAL G 271 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 281 through 286 removed outlier: 3.606A pdb=" N ARG G 283 " --> pdb=" O SER G 296 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL G 302 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE G 318 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU G 304 " --> pdb=" O THR G 316 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 16 through 21 removed outlier: 6.747A pdb=" N CYS H 31 " --> pdb=" O HIS H 17 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA H 19 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA H 29 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N MET H 21 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG H 27 " --> pdb=" O MET H 21 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL H 37 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ASP H 52 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE H 39 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 60 through 65 removed outlier: 6.895A pdb=" N CYS H 77 " --> pdb=" O TRP H 61 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL H 63 " --> pdb=" O ALA H 75 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA H 75 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP H 65 " --> pdb=" O ILE H 73 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE H 73 " --> pdb=" O TRP H 65 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG H 87 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LYS H 95 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU H 89 " --> pdb=" O TRP H 93 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TRP H 93 " --> pdb=" O GLU H 89 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 106 through 111 removed outlier: 6.213A pdb=" N GLN H 139 " --> pdb=" O THR H 135 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 153 through 158 removed outlier: 5.785A pdb=" N LYS H 195 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLU H 204 " --> pdb=" O LYS H 195 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 215 through 220 removed outlier: 4.604A pdb=" N ARG H 239 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS H 259 " --> pdb=" O VAL H 240 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE H 242 " --> pdb=" O LEU H 257 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU H 257 " --> pdb=" O ILE H 242 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 265 through 270 Processing sheet with id=AE4, first strand: chain 'L' and resid 356 through 359 removed outlier: 3.657A pdb=" N HIS L 373 " --> pdb=" O CYS L 370 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU L 374 " --> pdb=" O ILE O 7 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 734 through 736 removed outlier: 4.374A pdb=" N HIS M 716 " --> pdb=" O SER L 736 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG M 724 " --> pdb=" O CYS M 719 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 833 through 835 removed outlier: 3.696A pdb=" N PHE L 824 " --> pdb=" O TRP M 756 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 342 through 345 removed outlier: 3.791A pdb=" N ALA M 355 " --> pdb=" O ALA M 396 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU M 397 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG Q 5 " --> pdb=" O VAL M 399 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 541 through 545 removed outlier: 3.603A pdb=" N THR N 554 " --> pdb=" O LYS N 646 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS N 646 " --> pdb=" O THR N 554 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 935 through 937 Processing sheet with id=AF1, first strand: chain 'O' and resid 15 through 20 removed outlier: 6.618A pdb=" N CYS O 30 " --> pdb=" O HIS O 16 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL O 18 " --> pdb=" O ALA O 28 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA O 28 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER O 35 " --> pdb=" O SER O 31 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP O 40 " --> pdb=" O CYS O 49 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N CYS O 49 " --> pdb=" O ASP O 40 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 60 through 65 removed outlier: 3.760A pdb=" N ARG O 62 " --> pdb=" O CYS O 77 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA O 83 " --> pdb=" O THR O 108 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N THR O 108 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL O 85 " --> pdb=" O ARG O 106 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 116 through 121 removed outlier: 3.585A pdb=" N ASP O 118 " --> pdb=" O CYS O 133 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE O 138 " --> pdb=" O SER O 134 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS O 157 " --> pdb=" O ILE O 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLU O 143 " --> pdb=" O LEU O 155 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU O 155 " --> pdb=" O GLU O 143 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 165 through 170 removed outlier: 3.814A pdb=" N CYS O 167 " --> pdb=" O GLY O 185 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL O 197 " --> pdb=" O THR O 214 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR O 214 " --> pdb=" O VAL O 197 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE O 199 " --> pdb=" O ALA O 212 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 224 through 227 removed outlier: 3.560A pdb=" N ASP O 224 " --> pdb=" O ALA O 241 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL O 245 " --> pdb=" O GLN O 273 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN O 273 " --> pdb=" O VAL O 245 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE O 247 " --> pdb=" O VAL O 271 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS O 269 " --> pdb=" O THR O 249 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 283 through 286 removed outlier: 6.587A pdb=" N VAL O 302 " --> pdb=" O ILE O 318 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE O 318 " --> pdb=" O VAL O 302 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU O 304 " --> pdb=" O THR O 316 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 4 through 7 removed outlier: 4.664A pdb=" N LEU T 374 " --> pdb=" O ILE P 7 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 15 through 20 removed outlier: 3.723A pdb=" N ASP P 17 " --> pdb=" O CYS P 30 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER P 35 " --> pdb=" O SER P 31 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 15 through 20 removed outlier: 3.723A pdb=" N ASP P 17 " --> pdb=" O CYS P 30 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER P 35 " --> pdb=" O SER P 31 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 60 through 62 removed outlier: 3.557A pdb=" N ARG P 62 " --> pdb=" O CYS P 77 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR P 82 " --> pdb=" O SER P 78 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU P 109 " --> pdb=" O ALA P 83 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL P 85 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR P 107 " --> pdb=" O VAL P 85 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 116 through 119 removed outlier: 3.590A pdb=" N ASP P 118 " --> pdb=" O CYS P 133 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR P 142 " --> pdb=" O LEU P 130 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS P 157 " --> pdb=" O ILE P 141 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU P 143 " --> pdb=" O LEU P 155 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU P 155 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 168 through 170 removed outlier: 3.737A pdb=" N GLN P 198 " --> pdb=" O VAL P 184 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE P 199 " --> pdb=" O ALA P 212 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 224 through 227 removed outlier: 3.996A pdb=" N ASP P 224 " --> pdb=" O ALA P 241 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS P 236 " --> pdb=" O LEU P 250 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL P 245 " --> pdb=" O GLN P 273 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLN P 273 " --> pdb=" O VAL P 245 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE P 247 " --> pdb=" O VAL P 271 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL P 271 " --> pdb=" O ILE P 247 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS P 269 " --> pdb=" O THR P 249 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 281 through 286 removed outlier: 6.360A pdb=" N SER P 296 " --> pdb=" O TRP P 282 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL P 284 " --> pdb=" O ALA P 294 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA P 294 " --> pdb=" O VAL P 284 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP P 286 " --> pdb=" O VAL P 292 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL P 292 " --> pdb=" O TRP P 286 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY P 297 " --> pdb=" O CYS P 301 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N CYS P 301 " --> pdb=" O GLY P 297 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL P 302 " --> pdb=" O ILE P 318 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE P 318 " --> pdb=" O VAL P 302 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU P 304 " --> pdb=" O THR P 316 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 15 through 20 removed outlier: 4.391A pdb=" N SER Q 35 " --> pdb=" O SER Q 31 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL Q 36 " --> pdb=" O SER Q 52 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER Q 52 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL Q 38 " --> pdb=" O THR Q 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 60 through 65 removed outlier: 3.563A pdb=" N ARG Q 62 " --> pdb=" O CYS Q 77 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA Q 83 " --> pdb=" O THR Q 108 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N THR Q 108 " --> pdb=" O ALA Q 83 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 106 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 116 through 121 removed outlier: 3.661A pdb=" N ASP Q 118 " --> pdb=" O CYS Q 133 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE Q 138 " --> pdb=" O SER Q 134 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU Q 143 " --> pdb=" O LEU Q 155 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU Q 155 " --> pdb=" O GLU Q 143 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 165 through 170 removed outlier: 7.569A pdb=" N VAL Q 197 " --> pdb=" O THR Q 214 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N THR Q 214 " --> pdb=" O VAL Q 197 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE Q 199 " --> pdb=" O ALA Q 212 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS Q 208 " --> pdb=" O ASN Q 203 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 224 through 227 removed outlier: 3.792A pdb=" N ASP Q 224 " --> pdb=" O ALA Q 241 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR Q 249 " --> pdb=" O ILE Q 270 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE Q 270 " --> pdb=" O THR Q 249 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LYS Q 251 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE Q 268 " --> pdb=" O LYS Q 251 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 281 through 286 removed outlier: 6.799A pdb=" N SER Q 296 " --> pdb=" O TRP Q 282 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL Q 284 " --> pdb=" O ALA Q 294 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA Q 294 " --> pdb=" O VAL Q 284 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TRP Q 286 " --> pdb=" O VAL Q 292 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL Q 292 " --> pdb=" O TRP Q 286 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY Q 297 " --> pdb=" O CYS Q 301 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS Q 301 " --> pdb=" O GLY Q 297 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY Q 317 " --> pdb=" O LEU Q 304 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS Q 306 " --> pdb=" O CYS Q 315 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N CYS Q 315 " --> pdb=" O LYS Q 306 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 16 through 21 removed outlier: 6.831A pdb=" N CYS R 31 " --> pdb=" O HIS R 17 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA R 19 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA R 29 " --> pdb=" O ALA R 19 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET R 21 " --> pdb=" O ARG R 27 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG R 27 " --> pdb=" O MET R 21 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP R 41 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU R 49 " --> pdb=" O ASP R 41 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'R' and resid 60 through 65 removed outlier: 6.880A pdb=" N CYS R 77 " --> pdb=" O TRP R 61 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL R 63 " --> pdb=" O ALA R 75 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA R 75 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TRP R 65 " --> pdb=" O ILE R 73 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE R 73 " --> pdb=" O TRP R 65 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ARG R 87 " --> pdb=" O LYS R 95 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS R 95 " --> pdb=" O ARG R 87 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLU R 89 " --> pdb=" O TRP R 93 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TRP R 93 " --> pdb=" O GLU R 89 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 106 through 111 removed outlier: 6.672A pdb=" N GLY R 123 " --> pdb=" O ASN R 107 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL R 109 " --> pdb=" O ALA R 121 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA R 121 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP R 111 " --> pdb=" O ILE R 119 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE R 119 " --> pdb=" O TRP R 111 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU R 131 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 153 through 158 removed outlier: 3.932A pdb=" N GLN R 206 " --> pdb=" O LEU R 193 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS R 195 " --> pdb=" O GLU R 204 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLU R 204 " --> pdb=" O LYS R 195 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 215 through 220 removed outlier: 3.743A pdb=" N ASP R 217 " --> pdb=" O CYS R 234 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG R 239 " --> pdb=" O SER R 235 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL R 240 " --> pdb=" O LEU R 258 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 265 through 270 Processing sheet with id=AH9, first strand: chain 'T' and resid 7 through 10 removed outlier: 3.667A pdb=" N SER T 26 " --> pdb=" O VAL T 20 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER T 55 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS T 29 " --> pdb=" O LEU T 53 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU T 53 " --> pdb=" O HIS T 29 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'T' and resid 63 through 67 Processing sheet with id=AI2, first strand: chain 'T' and resid 116 through 121 Processing sheet with id=AI3, first strand: chain 'T' and resid 189 through 192 removed outlier: 3.777A pdb=" N SER T 189 " --> pdb=" O GLY T 203 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU T 208 " --> pdb=" O VAL T 222 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL T 222 " --> pdb=" O LEU T 208 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET T 220 " --> pdb=" O ILE T 210 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP T 212 " --> pdb=" O GLN T 218 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLN T 218 " --> pdb=" O ASP T 212 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'T' and resid 228 through 232 removed outlier: 4.974A pdb=" N GLY T 229 " --> pdb=" O PHE T 243 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE T 243 " --> pdb=" O GLY T 229 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'T' and resid 228 through 232 removed outlier: 4.974A pdb=" N GLY T 229 " --> pdb=" O PHE T 243 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE T 243 " --> pdb=" O GLY T 229 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL T 240 " --> pdb=" O TRP T 251 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'T' and resid 270 through 272 removed outlier: 3.949A pdb=" N LYS T 272 " --> pdb=" O LEU T 286 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE T 314 " --> pdb=" O ASP T 297 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'T' and resid 337 through 341 Processing sheet with id=AI8, first strand: chain 'U' and resid 69 through 71 removed outlier: 4.167A pdb=" N GLU U 7 " --> pdb=" O GLU U 146 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'U' and resid 115 through 116 removed outlier: 6.261A pdb=" N ASP U 121 " --> pdb=" O VAL U 81 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL U 81 " --> pdb=" O ASP U 121 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL U 78 " --> pdb=" O HIS U 8 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N HIS U 8 " --> pdb=" O VAL U 78 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN U 80 " --> pdb=" O LEU U 6 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU U 6 " --> pdb=" O ASN U 80 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL U 55 " --> pdb=" O ARG U 11 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE U 41 " --> pdb=" O ASP U 56 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'U' and resid 263 through 264 Processing sheet with id=AJ2, first strand: chain 'V' and resid 69 through 71 removed outlier: 6.132A pdb=" N LEU V 3 " --> pdb=" O TYR V 144 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU V 146 " --> pdb=" O LEU V 3 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE V 5 " --> pdb=" O GLU V 146 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'V' and resid 112 through 116 removed outlier: 6.322A pdb=" N ASP V 121 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL V 81 " --> pdb=" O ASP V 121 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL V 78 " --> pdb=" O HIS V 8 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS V 8 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASN V 80 " --> pdb=" O LEU V 6 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU V 6 " --> pdb=" O ASN V 80 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'V' and resid 263 through 264 Processing sheet with id=AJ5, first strand: chain 'V' and resid 263 through 264 1904 hydrogen bonds defined for protein. 5307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.55 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9582 1.33 - 1.45: 10289 1.45 - 1.57: 24054 1.57 - 1.70: 1 1.70 - 1.82: 392 Bond restraints: 44318 Sorted by residual: bond pdb=" N MET U 265 " pdb=" CA MET U 265 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.18e-02 7.18e+03 7.99e+00 bond pdb=" N GLN U 271 " pdb=" CA GLN U 271 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.41e-02 5.03e+03 6.24e+00 bond pdb=" CG PRO B 684 " pdb=" CD PRO B 684 " ideal model delta sigma weight residual 1.503 1.425 0.078 3.40e-02 8.65e+02 5.24e+00 bond pdb=" N ASN B 84 " pdb=" CA ASN B 84 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.32e-02 5.74e+03 4.99e+00 bond pdb=" N VAL U 281 " pdb=" CA VAL U 281 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.64e-02 3.72e+03 4.77e+00 ... (remaining 44313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 59973 1.78 - 3.57: 588 3.57 - 5.35: 72 5.35 - 7.14: 10 7.14 - 8.92: 8 Bond angle restraints: 60651 Sorted by residual: angle pdb=" CA PRO B 684 " pdb=" N PRO B 684 " pdb=" CD PRO B 684 " ideal model delta sigma weight residual 112.00 104.08 7.92 1.40e+00 5.10e-01 3.20e+01 angle pdb=" N PRO B 684 " pdb=" CD PRO B 684 " pdb=" CG PRO B 684 " ideal model delta sigma weight residual 103.20 94.87 8.33 1.50e+00 4.44e-01 3.08e+01 angle pdb=" CA GLY U 270 " pdb=" C GLY U 270 " pdb=" O GLY U 270 " ideal model delta sigma weight residual 121.62 117.24 4.38 9.80e-01 1.04e+00 2.00e+01 angle pdb=" CA GLY U 270 " pdb=" C GLY U 270 " pdb=" N GLN U 271 " ideal model delta sigma weight residual 114.67 118.67 -4.00 1.11e+00 8.12e-01 1.30e+01 angle pdb=" C VAL U 281 " pdb=" N ALA U 282 " pdb=" CA ALA U 282 " ideal model delta sigma weight residual 120.38 115.31 5.07 1.46e+00 4.69e-01 1.20e+01 ... (remaining 60646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 23811 17.65 - 35.29: 1396 35.29 - 52.94: 215 52.94 - 70.58: 44 70.58 - 88.23: 10 Dihedral angle restraints: 25476 sinusoidal: 7909 harmonic: 17567 Sorted by residual: dihedral pdb=" CA ARG C 418 " pdb=" C ARG C 418 " pdb=" N TYR C 419 " pdb=" CA TYR C 419 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ARG M 418 " pdb=" C ARG M 418 " pdb=" N TYR M 419 " pdb=" CA TYR M 419 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA THR U 256 " pdb=" C THR U 256 " pdb=" N SER U 257 " pdb=" CA SER U 257 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 25473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 5768 0.050 - 0.099: 1016 0.099 - 0.149: 307 0.149 - 0.198: 6 0.198 - 0.248: 1 Chirality restraints: 7098 Sorted by residual: chirality pdb=" CA ILE U 268 " pdb=" N ILE U 268 " pdb=" C ILE U 268 " pdb=" CB ILE U 268 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ARG U 267 " pdb=" N ARG U 267 " pdb=" C ARG U 267 " pdb=" CB ARG U 267 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CG LEU N 728 " pdb=" CB LEU N 728 " pdb=" CD1 LEU N 728 " pdb=" CD2 LEU N 728 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.09e-01 ... (remaining 7095 not shown) Planarity restraints: 7677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 972 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C SER D 972 " -0.066 2.00e-02 2.50e+03 pdb=" O SER D 972 " 0.025 2.00e-02 2.50e+03 pdb=" N THR D 973 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 226 " 0.054 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO H 227 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO H 227 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 227 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 683 " 0.037 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO B 684 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 684 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 684 " 0.030 5.00e-02 4.00e+02 ... (remaining 7674 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1723 2.73 - 3.27: 43242 3.27 - 3.81: 73075 3.81 - 4.36: 86427 4.36 - 4.90: 150777 Nonbonded interactions: 355244 Sorted by model distance: nonbonded pdb=" N LEU B 787 " pdb="ZN ZN B 904 " model vdw 2.182 2.310 nonbonded pdb=" OD2 ASP L 405 " pdb=" NH1 ARG L 411 " model vdw 2.186 3.120 nonbonded pdb=" O ASP L 814 " pdb=" OG SER M 790 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR B 655 " pdb=" OD1 ASP B 657 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR U 47 " pdb=" O ASP U 50 " model vdw 2.211 3.040 ... (remaining 355239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'L' and ((resid 353 through 355 and (name N or name CA or name C or name \ O or name CB )) or resid 356 through 379 or (resid 386 through 388 and (name N o \ r name CA or name C or name O or name CB )) or resid 389 through 440 or resid 45 \ 0 through 460 or (resid 461 and (name N or name CA or name C or name O or name C \ B )) or resid 462 through 463 or (resid 464 and (name N or name CA or name C or \ name O or name CB )) or resid 483 through 532 or (resid 533 through 537 and (nam \ e N or name CA or name C or name O or name CB )) or resid 538 or (resid 539 and \ (name N or name CA or name C or name O or name CB )) or resid 540 through 565 or \ (resid 566 through 569 and (name N or name CA or name C or name O or name CB )) \ or resid 570 through 573 or (resid 574 through 575 and (name N or name CA or na \ me C or name O or name CB )) or resid 576 through 581 or (resid 582 and (name N \ or name CA or name C or name O or name CB )) or resid 583 or (resid 584 and (nam \ e N or name CA or name C or name O or name CB )) or resid 585 through 608 or (re \ sid 609 through 610 and (name N or name CA or name C or name O or name CB )) or \ resid 611 through 630 or (resid 631 and (name N or name CA or name C or name O o \ r name CB )) or resid 632 through 633 or (resid 634 through 635 and (name N or n \ ame CA or name C or name O or name CB )) or resid 636 through 638 or (resid 639 \ and (name N or name CA or name C or name O or name CB )) or resid 640 through 64 \ 1 or (resid 642 through 643 and (name N or name CA or name C or name O or name C \ B )) or resid 644 through 655 or (resid 656 and (name N or name CA or name C or \ name O or name CB )) or resid 657 through 662 or (resid 663 and (name N or name \ CA or name C or name O or name CB )) or resid 664 through 666 or (resid 667 and \ (name N or name CA or name C or name O or name CB )) or resid 668 through 684 or \ (resid 685 through 686 and (name N or name CA or name C or name O or name CB )) \ or resid 687 through 690 or (resid 691 and (name N or name CA or name C or name \ O or name CB )) or resid 692 through 741 or (resid 742 and (name N or name CA o \ r name C or name O or name CB )) or resid 743 through 746 or (resid 771 and (nam \ e N or name CA or name C or name O or name CB )) or resid 772 through 778 or (re \ sid 779 through 780 and (name N or name CA or name C or name O or name CB )) or \ resid 781 through 795 or (resid 796 and (name N or name CA or name C or name O o \ r name CB )) or resid 814 through 816 or (resid 817 through 818 and (name N or n \ ame CA or name C or name O or name CB )) or resid 819 through 1004)) } ncs_group { reference = (chain 'B' and (resid 5 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 13 or (resid 14 through 17 and (name \ N or name CA or name C or name O or name CB )) or resid 18 through 30 or resid 4 \ 3 through 53 or (resid 54 through 60 and (name N or name CA or name C or name O \ or name CB )) or resid 61 through 63 or (resid 64 through 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 through 76 or (resid 77 throug \ h 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throug \ h 83 or (resid 84 and (name N or name CA or name C or name O or name CB )) or re \ sid 85 through 86 or (resid 87 through 88 and (name N or name CA or name C or na \ me O or name CB )) or resid 89 or (resid 90 through 104 and (name N or name CA o \ r name C or name O or name CB )) or resid 105 or (resid 106 through 107 and (nam \ e N or name CA or name C or name O or name CB )) or resid 108 or (resid 109 and \ (name N or name CA or name C or name O or name CB )) or resid 110 through 116 or \ (resid 117 through 118 and (name N or name CA or name C or name O or name CB )) \ or resid 119 through 140 or (resid 141 through 142 and (name N or name CA or na \ me C or name O or name CB )) or resid 143 or (resid 144 and (name N or name CA o \ r name C or name O or name CB )) or resid 145 through 207 or (resid 208 through \ 210 and (name N or name CA or name C or name O or name CB )) or resid 211 throug \ h 223 or (resid 224 through 228 and (name N or name CA or name C or name O or na \ me CB )) or resid 229 through 232 or (resid 233 and (name N or name CA or name C \ or name O or name CB )) or resid 234 or (resid 235 through 242 and (name N or n \ ame CA or name C or name O or name CB )) or resid 243 through 249 or (resid 250 \ and (name N or name CA or name C or name O or name CB )) or resid 251 through 26 \ 2 or (resid 263 through 266 and (name N or name CA or name C or name O or name C \ B )) or resid 267 through 271 or (resid 272 and (name N or name CA or name C or \ name O or name CB )) or resid 273 through 285 or (resid 286 through 292 and (nam \ e N or name CA or name C or name O or name CB )) or resid 293 through 317 or (re \ sid 318 through 319 and (name N or name CA or name C or name O or name CB )) or \ resid 320 through 324 or (resid 325 through 327 and (name N or name CA or name C \ or name O or name CB )) or resid 328 through 337 or (resid 338 through 342 and \ (name N or name CA or name C or name O or name CB )) or resid 343 through 355 or \ (resid 356 through 359 and (name N or name CA or name C or name O or name CB )) \ or resid 360 through 373 or (resid 374 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 388 through 456 or (resid 457 and (name N \ or name CA or name C or name O or name CB )) or resid 458 through 460 or (resid \ 461 and (name N or name CA or name C or name O or name CB )) or resid 462 throug \ h 466 or (resid 467 through 468 and (name N or name CA or name C or name O or na \ me CB )) or resid 469 or (resid 470 through 471 and (name N or name CA or name C \ or name O or name CB )) or resid 472 or (resid 473 and (name N or name CA or na \ me C or name O or name CB )) or resid 474 through 534 or (resid 535 through 537 \ and (name N or name CA or name C or name O or name CB )) or resid 538 through 54 \ 1 or (resid 542 through 543 and (name N or name CA or name C or name O or name C \ B )) or resid 544 through 545 or resid 552 through 554 or (resid 555 and (name N \ or name CA or name C or name O or name CB )) or resid 556 through 565 or (resid \ 566 through 569 and (name N or name CA or name C or name O or name CB )) or res \ id 570 through 727 or (resid 728 and (name N or name CA or name C or name O or n \ ame CB )) or resid 783 through 903)) selection = (chain 'T' and (resid 5 through 18 or (resid 19 through 26 and (name N or name C \ A or name C or name O or name CB )) or resid 27 through 46 or resid 49 through 5 \ 5 or (resid 56 through 60 and (name N or name CA or name C or name O or name CB \ )) or resid 61 through 92 or resid 100 through 148 or resid 174 through 180 or ( \ resid 181 and (name N or name CA or name C or name O or name CB )) or resid 182 \ through 183 or (resid 184 through 187 and (name N or name CA or name C or name O \ or name CB )) or resid 188 through 212 or (resid 213 through 216 and (name N or \ name CA or name C or name O or name CB )) or resid 219 through 270 or (resid 27 \ 1 through 272 and (name N or name CA or name C or name O or name CB )) or resid \ 273 through 274 or (resid 275 through 276 and (name N or name CA or name C or na \ me O or name CB )) or resid 277 through 294 or (resid 295 through 299 and (name \ N or name CA or name C or name O or name CB )) or resid 313 through 354 or (resi \ d 355 through 359 and (name N or name CA or name C or name O or name CB )) or re \ sid 360 through 398 or (resid 399 and (name N or name CA or name C or name O or \ name CB )) or resid 400 or (resid 401 and (name N or name CA or name C or name O \ or name CB )) or resid 402 through 403 or (resid 404 through 408 and (name N or \ name CA or name C or name O or name CB )) or resid 409 through 410 or (resid 41 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 412 through \ 413 or (resid 414 through 416 and (name N or name CA or name C or name O or name \ CB )) or resid 417 or resid 420 through 423 or (resid 424 and (name N or name C \ A or name C or name O or name CB )) or resid 425 through 438 or (resid 451 and ( \ name N or name CA or name C or name O or name CB )) or resid 452 through 685 or \ (resid 686 and (name N or name CA or name C or name O or name CB )) or resid 687 \ through 728 or resid 783 through 792 or (resid 819 and (name N or name CA or na \ me C or name O or name CB )) or resid 820 through 825 or (resid 826 and (name N \ or name CA or name C or name O or name CB )) or resid 827 or (resid 828 and (nam \ e N or name CA or name C or name O or name CB )) or resid 829 through 856 or (re \ sid 857 and (name N or name CA or name C or name O or name CB )) or resid 858 th \ rough 859 or (resid 860 and (name N or name CA or name C or name O or name CB )) \ or resid 861 or (resid 862 through 863 and (name N or name CA or name C or name \ O or name CB )) or resid 901 through 903)) } ncs_group { reference = chain 'C' selection = (chain 'M' and (resid 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB )) or resid 342 through 346 or (resid 347 and (name N or name CA o \ r name C or name O or name CB )) or resid 348 through 349 or (resid 350 through \ 352 and (name N or name CA or name C or name O or name CB )) or resid 353 or (re \ sid 397 and (name N or name CA or name C or name O or name CB )) or resid 398 or \ (resid 399 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 0 or (resid 401 and (name N or name CA or name C or name O or name CB )) or resi \ d 402 or resid 409 or (resid 410 and (name N or name CA or name C or name O or n \ ame CB )) or resid 411 through 416 or (resid 417 and (name N or name CA or name \ C or name O or name CB )) or resid 418 through 427 or (resid 428 and (name N or \ name CA or name C or name O or name CB )) or resid 429 through 430 or (resid 431 \ and (name N or name CA or name C or name O or name CB )) or resid 432 through 4 \ 34 or (resid 435 and (name N or name CA or name C or name O or name CB )) or res \ id 436 through 438 or (resid 439 and (name N or name CA or name C or name O or n \ ame CB )) or resid 440 through 458 or resid 627 through 630 or (resid 631 and (n \ ame N or name CA or name C or name O or name CB )) or resid 632 through 637 or ( \ resid 638 through 639 and (name N or name CA or name C or name O or name CB )) o \ r resid 640 through 645 or (resid 646 and (name N or name CA or name C or name O \ or name CB )) or resid 647 through 666 or (resid 667 and (name N or name CA or \ name C or name O or name CB )) or resid 668 through 670 or (resid 671 and (name \ N or name CA or name C or name O or name CB )) or resid 672 through 673 or (resi \ d 674 and (name N or name CA or name C or name O or name CB )) or resid 675 thro \ ugh 681 or (resid 682 and (name N or name CA or name C or name O or name CB )) o \ r resid 683 through 687 or (resid 688 and (name N or name CA or name C or name O \ or name CB )) or resid 689 through 694 or (resid 695 and (name N or name CA or \ name C or name O or name CB )) or resid 696 through 699 or (resid 700 and (name \ N or name CA or name C or name O or name CB )) or resid 701 through 705 or (resi \ d 706 through 708 and (name N or name CA or name C or name O or name CB )) or re \ sid 709 through 710 or resid 712 through 720 or (resid 721 and (name N or name C \ A or name C or name O or name CB )) or resid 722 or (resid 723 through 724 and ( \ name N or name CA or name C or name O or name CB )) or resid 725 through 727 or \ (resid 728 through 729 and (name N or name CA or name C or name O or name CB )) \ or resid 730 through 731 or (resid 732 and (name N or name CA or name C or name \ O or name CB )) or resid 733 or (resid 734 through 735 and (name N or name CA or \ name C or name O or name CB )) or resid 736 or (resid 737 through 738 and (name \ N or name CA or name C or name O or name CB )) or resid 739 through 750 or (res \ id 751 and (name N or name CA or name C or name O or name CB )) or resid 752 thr \ ough 769 or (resid 770 through 771 and (name N or name CA or name C or name O or \ name CB )) or resid 772 through 773 or (resid 774 and (name N or name CA or nam \ e C or name O or name CB )) or resid 775 through 785 or (resid 786 and (name N o \ r name CA or name C or name O or name CB )) or resid 787 or (resid 788 and (name \ N or name CA or name C or name O or name CB )) or resid 789 or (resid 790 and ( \ name N or name CA or name C or name O or name CB )) or resid 1001 through 1004)) \ } ncs_group { reference = (chain 'D' and (resid 533 through 709 or (resid 710 and (name N or name CA or na \ me C or name O or name CB )) or resid 711 through 1003)) selection = (chain 'N' and ((resid 533 through 534 and (name N or name CA or name C or name \ O or name CB )) or resid 535 or (resid 536 and (name N or name CA or name C or n \ ame O or name CB )) or resid 537 through 539 or (resid 540 and (name N or name C \ A or name C or name O or name CB )) or resid 541 through 544 or (resid 545 and ( \ name N or name CA or name C or name O or name CB )) or resid 546 through 553 or \ (resid 554 through 555 and (name N or name CA or name C or name O or name CB )) \ or resid 556 or resid 645 or (resid 646 and (name N or name CA or name C or name \ O or name CB )) or resid 647 through 649 or (resid 650 through 651 and (name N \ or name CA or name C or name O or name CB )) or resid 652 through 659 or (resid \ 660 and (name N or name CA or name C or name O or name CB )) or resid 661 throug \ h 663 or (resid 664 through 665 and (name N or name CA or name C or name O or na \ me CB )) or resid 666 or (resid 667 and (name N or name CA or name C or name O o \ r name CB )) or resid 668 or (resid 669 through 672 and (name N or name CA or na \ me C or name O or name CB )) or resid 673 or (resid 674 through 675 and (name N \ or name CA or name C or name O or name CB )) or resid 676 through 677 or (resid \ 678 through 679 and (name N or name CA or name C or name O or name CB )) or resi \ d 680 through 684 or (resid 685 through 686 and (name N or name CA or name C or \ name O or name CB )) or resid 687 through 704 or (resid 705 and (name N or name \ CA or name C or name O or name CB )) or resid 706 through 713 or (resid 714 thro \ ugh 716 and (name N or name CA or name C or name O or name CB )) or resid 717 th \ rough 729 or (resid 730 and (name N or name CA or name C or name O or name CB )) \ or resid 731 through 737 or (resid 738 and (name N or name CA or name C or name \ O or name CB )) or resid 739 through 752 or (resid 753 through 757 and (name N \ or name CA or name C or name O or name CB )) or (resid 838 through 842 and (name \ N or name CA or name C or name O or name CB )) or resid 843 through 844 or (res \ id 845 through 846 and (name N or name CA or name C or name O or name CB )) or r \ esid 847 through 856 or (resid 857 through 858 and (name N or name CA or name C \ or name O or name CB )) or resid 859 or (resid 860 through 861 and (name N or na \ me CA or name C or name O or name CB )) or resid 862 through 863 or (resid 864 a \ nd (name N or name CA or name C or name O or name CB )) or resid 865 through 875 \ or (resid 876 through 878 and (name N or name CA or name C or name O or name CB \ )) or resid 879 through 880 or (resid 881 and (name N or name CA or name C or n \ ame O or name CB )) or resid 882 through 888 or (resid 922 and (name N or name C \ A or name C or name O or name CB )) or resid 923 through 928 or (resid 929 throu \ gh 930 and (name N or name CA or name C or name O or name CB )) or resid 931 or \ (resid 932 and (name N or name CA or name C or name O or name CB )) or resid 933 \ through 938 or (resid 939 and (name N or name CA or name C or name O or name CB \ )) or resid 940 through 950 or (resid 951 through 952 and (name N or name CA or \ name C or name O or name CB )) or resid 953 through 955 or (resid 956 through 9 \ 58 and (name N or name CA or name C or name O or name CB )) or resid 959 through \ 961 or (resid 962 and (name N or name CA or name C or name O or name CB )) or r \ esid 963 through 969 or (resid 970 through 971 and (name N or name CA or name C \ or name O or name CB )) or resid 972 through 1003)) } ncs_group { reference = (chain 'E' and ((resid 15 through 19 and (name N or name CA or name C or name O \ or name CB )) or resid 20 or (resid 21 and (name N or name CA or name C or name \ O or name CB )) or resid 22 through 25 or (resid 26 through 40 and (name N or na \ me CA or name C or name O or name CB )) or resid 47 through 48 or (resid 49 thro \ ugh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thro \ ugh 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or \ (resid 60 through 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 71 or (resid 72 through 85 and (name N or name CA or name C or \ name O or name CB )) or resid 86 through 88 or (resid 89 through 102 and (name \ N or name CA or name C or name O or name CB )) or resid 103 or (resid 104 throug \ h 120 and (name N or name CA or name C or name O or name CB )) or resid 121 thro \ ugh 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) o \ r resid 127 or (resid 128 and (name N or name CA or name C or name O or name CB \ )) or resid 129 or (resid 130 through 134 and (name N or name CA or name C or na \ me O or name CB )) or (resid 137 through 144 and (name N or name CA or name C or \ name O or name CB )) or resid 145 through 146 or (resid 147 through 149 and (na \ me N or name CA or name C or name O or name CB )) or resid 150 through 152 or (r \ esid 153 through 160 and (name N or name CA or name C or name O or name CB )) or \ (resid 166 through 169 and (name N or name CA or name C or name O or name CB )) \ or resid 170 or (resid 171 and (name N or name CA or name C or name O or name C \ B )) or resid 172 or (resid 173 and (name N or name CA or name C or name O or na \ me CB )) or resid 174 through 178 or (resid 179 and (name N or name CA or name C \ or name O or name CB )) or resid 180 or (resid 181 through 184 and (name N or n \ ame CA or name C or name O or name CB )) or resid 185 or (resid 186 through 205 \ and (name N or name CA or name C or name O or name CB )) or resid 206 through 20 \ 8 or (resid 209 through 210 and (name N or name CA or name C or name O or name C \ B )) or resid 220 through 221 or (resid 222 through 226 and (name N or name CA o \ r name C or name O or name CB )) or resid 227 through 239 or (resid 240 through \ 251 and (name N or name CA or name C or name O or name CB )) or resid 252 or (re \ sid 277 through 285 and (name N or name CA or name C or name O or name CB )) or \ resid 286 through 294 or (resid 295 through 296 and (name N or name CA or name C \ or name O or name CB )) or (resid 297 through 304 and (name N or name CA or nam \ e C or name O or name CB )) or resid 305 through 314 or (resid 315 through 316 a \ nd (name N or name CA or name C or name O or name CB )) or resid 317 or (resid 3 \ 18 through 320 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 15 through 26 or (resid 27 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 89 or resid 101 through \ 151 or (resid 152 through 169 and (name N or name CA or name C or name O or nam \ e CB )) or resid 170 through 204 or (resid 205 and (name N or name CA or name C \ or name O or name CB )) or resid 206 through 281 or (resid 282 through 285 and ( \ name N or name CA or name C or name O or name CB )) or resid 286 through 308 or \ resid 312 through 320)) selection = (chain 'G' and ((resid 15 through 19 and (name N or name CA or name C or name O \ or name CB )) or resid 20 or (resid 21 and (name N or name CA or name C or name \ O or name CB )) or resid 22 through 25 or (resid 26 through 40 and (name N or na \ me CA or name C or name O or name CB )) or resid 47 through 48 or (resid 49 thro \ ugh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thro \ ugh 54 or (resid 55 through 56 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 60 through 64 and (name N or name CA or name C or name O or na \ me CB )) or resid 65 through 71 or (resid 72 through 85 and (name N or name CA o \ r name C or name O or name CB )) or resid 86 or (resid 87 through 89 and (name N \ or name CA or name C or name O or name CB )) or (resid 101 through 102 and (nam \ e N or name CA or name C or name O or name CB )) or resid 103 or (resid 104 thro \ ugh 120 and (name N or name CA or name C or name O or name CB )) or resid 121 th \ rough 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) \ or resid 127 or (resid 128 and (name N or name CA or name C or name O or name C \ B )) or resid 129 or (resid 130 through 134 and (name N or name CA or name C or \ name O or name CB )) or resid 137 or (resid 138 through 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 146 or (resid 147 thro \ ugh 149 and (name N or name CA or name C or name O or name CB )) or resid 150 or \ (resid 151 through 160 and (name N or name CA or name C or name O or name CB )) \ or (resid 166 through 169 and (name N or name CA or name C or name O or name CB \ )) or resid 170 or (resid 171 and (name N or name CA or name C or name O or nam \ e CB )) or resid 172 or (resid 173 and (name N or name CA or name C or name O or \ name CB )) or resid 174 through 178 or (resid 179 and (name N or name CA or nam \ e C or name O or name CB )) or resid 180 or (resid 181 through 184 and (name N o \ r name CA or name C or name O or name CB )) or resid 185 or (resid 186 through 1 \ 87 and (name N or name CA or name C or name O or name CB )) or (resid 196 throug \ h 205 and (name N or name CA or name C or name O or name CB )) or resid 206 thro \ ugh 208 or (resid 209 through 210 and (name N or name CA or name C or name O or \ name CB )) or resid 220 through 221 or (resid 222 through 226 and (name N or nam \ e CA or name C or name O or name CB )) or resid 227 through 239 or (resid 240 th \ rough 251 and (name N or name CA or name C or name O or name CB )) or resid 252 \ or (resid 277 through 285 and (name N or name CA or name C or name O or name CB \ )) or resid 286 through 294 or (resid 295 through 296 and (name N or name CA or \ name C or name O or name CB )) or (resid 297 through 299 and (name N or name CA \ or name C or name O or name CB )) or resid 300 or (resid 301 through 304 and (na \ me N or name CA or name C or name O or name CB )) or resid 305 through 307 or (r \ esid 308 and (name N or name CA or name C or name O or name CB )) or (resid 312 \ and (name N or name CA or name C or name O or name CB )) or resid 313 through 31 \ 4 or (resid 315 through 316 and (name N or name CA or name C or name O or name C \ B )) or resid 317 or (resid 318 through 320 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'O' and ((resid 15 through 19 and (name N or name CA or name C or name O \ or name CB )) or resid 20 or (resid 21 and (name N or name CA or name C or name \ O or name CB )) or resid 22 through 24 or (resid 25 through 40 and (name N or na \ me CA or name C or name O or name CB )) or resid 47 or (resid 48 through 52 and \ (name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 th \ rough 56 and (name N or name CA or name C or name O or name CB )) or (resid 60 t \ hrough 64 and (name N or name CA or name C or name O or name CB )) or resid 65 t \ hrough 68 or (resid 69 and (name N or name CA or name C or name O or name CB )) \ or resid 70 through 71 or (resid 72 through 85 and (name N or name CA or name C \ or name O or name CB )) or resid 86 or (resid 87 through 89 and (name N or name \ CA or name C or name O or name CB )) or (resid 101 through 102 and (name N or na \ me CA or name C or name O or name CB )) or resid 103 or (resid 104 through 120 a \ nd (name N or name CA or name C or name O or name CB )) or resid 121 through 123 \ or (resid 124 and (name N or name CA or name C or name O or name CB )) or resid \ 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) or r \ esid 127 or (resid 128 and (name N or name CA or name C or name O or name CB )) \ or resid 129 or (resid 130 through 134 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 144 and (name N or name CA or \ name C or name O or name CB )) or resid 145 or (resid 146 through 149 and (name \ N or name CA or name C or name O or name CB )) or resid 150 or (resid 151 throu \ gh 160 and (name N or name CA or name C or name O or name CB )) or (resid 166 th \ rough 169 and (name N or name CA or name C or name O or name CB )) or resid 170 \ or (resid 171 and (name N or name CA or name C or name O or name CB )) or resid \ 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or re \ sid 174 through 178 or (resid 179 and (name N or name CA or name C or name O or \ name CB )) or resid 180 or (resid 181 through 184 and (name N or name CA or name \ C or name O or name CB )) or resid 185 or (resid 186 through 187 and (name N or \ name CA or name C or name O or name CB )) or (resid 196 through 205 and (name N \ or name CA or name C or name O or name CB )) or resid 206 or (resid 207 through \ 210 and (name N or name CA or name C or name O or name CB )) or (resid 220 and \ (name N or name CA or name C or name O or name CB )) or resid 221 or (resid 222 \ through 226 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 7 through 239 or (resid 240 through 251 and (name N or name CA or name C or name \ O or name CB )) or resid 252 or (resid 277 through 285 and (name N or name CA o \ r name C or name O or name CB )) or resid 286 through 294 or (resid 295 through \ 296 and (name N or name CA or name C or name O or name CB )) or resid 297 or (re \ sid 298 through 299 and (name N or name CA or name C or name O or name CB )) or \ resid 300 or (resid 301 through 304 and (name N or name CA or name C or name O o \ r name CB )) or resid 305 or (resid 306 through 308 and (name N or name CA or na \ me C or name O or name CB )) or (resid 312 and (name N or name CA or name C or n \ ame O or name CB )) or resid 313 or (resid 314 through 316 and (name N or name C \ A or name C or name O or name CB )) or resid 317 or (resid 318 through 320 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 15 through 40 or resid 47 through 56 or resid 60 through 7 \ 1 or (resid 72 through 85 and (name N or name CA or name C or name O or name CB \ )) or resid 86 through 89 or resid 101 through 134 or resid 137 through 151 or ( \ resid 152 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 166 through 204 or (resid 205 and (name N or name CA or name C or name O \ or name CB )) or resid 206 through 210 or resid 220 through 252 or resid 277 th \ rough 308 or resid 312 through 320)) selection = (chain 'Q' and ((resid 15 through 19 and (name N or name CA or name C or name O \ or name CB )) or resid 20 or (resid 21 and (name N or name CA or name C or name \ O or name CB )) or resid 22 through 24 or (resid 25 through 40 and (name N or na \ me CA or name C or name O or name CB )) or resid 47 or (resid 48 through 52 and \ (name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 th \ rough 56 and (name N or name CA or name C or name O or name CB )) or (resid 60 t \ hrough 64 and (name N or name CA or name C or name O or name CB )) or resid 65 t \ hrough 68 or (resid 69 and (name N or name CA or name C or name O or name CB )) \ or resid 70 through 71 or (resid 72 through 85 and (name N or name CA or name C \ or name O or name CB )) or resid 86 or (resid 87 through 89 and (name N or name \ CA or name C or name O or name CB )) or (resid 101 through 102 and (name N or na \ me CA or name C or name O or name CB )) or resid 103 or (resid 104 through 120 a \ nd (name N or name CA or name C or name O or name CB )) or resid 121 through 123 \ or (resid 124 and (name N or name CA or name C or name O or name CB )) or resid \ 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) or r \ esid 127 or (resid 128 and (name N or name CA or name C or name O or name CB )) \ or resid 129 or (resid 130 through 134 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 144 and (name N or name CA or \ name C or name O or name CB )) or resid 145 or (resid 146 through 149 and (name \ N or name CA or name C or name O or name CB )) or resid 150 or (resid 151 throu \ gh 160 and (name N or name CA or name C or name O or name CB )) or (resid 166 th \ rough 169 and (name N or name CA or name C or name O or name CB )) or resid 170 \ or (resid 171 and (name N or name CA or name C or name O or name CB )) or resid \ 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or re \ sid 174 through 178 or (resid 179 and (name N or name CA or name C or name O or \ name CB )) or resid 180 or (resid 181 through 184 and (name N or name CA or name \ C or name O or name CB )) or resid 185 or (resid 186 through 187 and (name N or \ name CA or name C or name O or name CB )) or (resid 196 through 205 and (name N \ or name CA or name C or name O or name CB )) or resid 206 through 207 or (resid \ 208 through 210 and (name N or name CA or name C or name O or name CB )) or (re \ sid 220 and (name N or name CA or name C or name O or name CB )) or resid 221 or \ (resid 222 through 226 and (name N or name CA or name C or name O or name CB )) \ or resid 227 through 239 or (resid 240 through 251 and (name N or name CA or na \ me C or name O or name CB )) or resid 252 or (resid 277 through 285 and (name N \ or name CA or name C or name O or name CB )) or resid 286 through 294 or (resid \ 295 through 296 and (name N or name CA or name C or name O or name CB )) or resi \ d 297 or (resid 298 through 299 and (name N or name CA or name C or name O or na \ me CB )) or resid 300 or (resid 301 through 304 and (name N or name CA or name C \ or name O or name CB )) or resid 305 or (resid 306 through 308 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 312 and (name N or name CA or \ name C or name O or name CB )) or resid 313 or (resid 314 through 316 and (name \ N or name CA or name C or name O or name CB )) or resid 317 or (resid 318 throu \ gh 320 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'H' selection = (chain 'R' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 8 or (resid 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 34 or (resid 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 42 or (resid 43 throug \ h 44 and (name N or name CA or name C or name O or name CB )) or resid 45 throug \ h 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or re \ sid 58 through 80 or (resid 81 through 82 and (name N or name CA or name C or na \ me O or name CB )) or resid 83 through 86 or (resid 87 and (name N or name CA or \ name C or name O or name CB )) or resid 88 through 89 or (resid 90 and (name N \ or name CA or name C or name O or name CB )) or resid 91 through 94 or (resid 95 \ and (name N or name CA or name C or name O or name CB )) or resid 96 through 97 \ or (resid 98 and (name N or name CA or name C or name O or name CB )) or resid \ 99 through 102 or (resid 103 and (name N or name CA or name C or name O or name \ CB )) or resid 104 through 138 or (resid 139 and (name N or name CA or name C or \ name O or name CB )) or resid 140 or (resid 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 or (resid 143 through 151 and (name N or \ name CA or name C or name O or name CB )) or resid 152 through 163 or (resid 177 \ and (name N or name CA or name C or name O or name CB )) or resid 178 through 1 \ 89 or (resid 190 and (name N or name CA or name C or name O or name CB )) or res \ id 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 194 or (resid 195 and (name N or name CA or name C or name O \ or name CB )) or resid 196 through 198 or (resid 199 and (name N or name CA or n \ ame C or name O or name CB )) or resid 200 through 203 or (resid 204 through 207 \ and (name N or name CA or name C or name O or name CB )) or resid 208 through 2 \ 12 or (resid 213 and (name N or name CA or name C or name O or name CB )) or res \ id 214 through 238 or (resid 239 and (name N or name CA or name C or name O or n \ ame CB )) or resid 240 through 246 or resid 250 or (resid 251 and (name N or nam \ e CA or name C or name O or name CB )) or resid 252 through 289 or (resid 290 an \ d (name N or name CA or name C or name O or name CB )) or resid 291 or resid 296 \ through 301)) } ncs_group { reference = (chain 'U' and (resid 1 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 82 or resid 96 through 148 or resid \ 150 through 189 or (resid 190 and (name N or name CA or name C or name O or nam \ e CB )) or resid 191 through 256 or (resid 257 and (name N or name CA or name C \ or name O or name CB )) or resid 258 through 266 or (resid 267 and (name N or na \ me CA or name C or name O or name CB )) or resid 268 through 270 or resid 279 th \ rough 292 or (resid 293 through 295 and (name N or name CA or name C or name O o \ r name CB )) or resid 296 through 320)) selection = (chain 'V' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 133 or (resid 134 and (name N or \ name CA or name C or name O or name CB )) or resid 135 through 142 or (resid 143 \ and (name N or name CA or name C or name O or name CB )) or resid 144 through 1 \ 45 or (resid 146 through 147 and (name N or name CA or name C or name O or name \ CB )) or resid 149 through 154 or (resid 175 and (name N or name CA or name C or \ name O or name CB )) or resid 176 through 270 or resid 279 through 282 or (resi \ d 283 and (name N or name CA or name C or name O or name CB )) or resid 284 thro \ ugh 312 or (resid 313 and (name N or name CA or name C or name O or name CB )) o \ r resid 314 or (resid 315 through 319 and (name N or name CA or name C or name O \ or name CB )) or resid 320)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.460 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: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 47.710 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 44431 Z= 0.106 Angle : 0.474 8.924 60757 Z= 0.253 Chirality : 0.041 0.248 7098 Planarity : 0.003 0.083 7677 Dihedral : 11.817 88.227 13998 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.63 % Favored : 97.25 % Rotamer: Outliers : 0.18 % Allowed : 0.10 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.12), residues: 5849 helix: 1.60 (0.13), residues: 1546 sheet: -0.38 (0.15), residues: 1427 loop : 0.06 (0.12), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 87 TYR 0.033 0.001 TYR M 419 PHE 0.019 0.001 PHE D 862 TRP 0.021 0.001 TRP R 220 HIS 0.005 0.001 HIS G 277 Details of bonding type rmsd covalent geometry : bond 0.00215 (44318) covalent geometry : angle 0.46640 (60651) hydrogen bonds : bond 0.21450 ( 1883) hydrogen bonds : angle 7.96581 ( 5307) metal coordination : bond 0.00575 ( 113) metal coordination : angle 2.08229 ( 106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 495 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 839 MET cc_start: 0.8023 (mmt) cc_final: 0.6483 (mpp) REVERT: C 414 ASP cc_start: 0.7680 (t0) cc_final: 0.7326 (t0) REVERT: D 868 GLU cc_start: 0.7368 (tp30) cc_final: 0.7077 (tp30) REVERT: F 103 TRP cc_start: 0.5268 (m-10) cc_final: 0.4948 (m-90) REVERT: F 175 SER cc_start: 0.8477 (m) cc_final: 0.8166 (t) REVERT: G 201 GLU cc_start: 0.7421 (tt0) cc_final: 0.7154 (tt0) REVERT: H 24 TYR cc_start: 0.7897 (m-80) cc_final: 0.7685 (m-80) REVERT: H 196 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6333 (tm-30) REVERT: M 410 ARG cc_start: 0.7030 (tpt170) cc_final: 0.6471 (tpt170) REVERT: M 414 ASP cc_start: 0.7630 (m-30) cc_final: 0.7093 (m-30) REVERT: M 640 MET cc_start: 0.8721 (tmm) cc_final: 0.8207 (tmm) REVERT: M 726 MET cc_start: 0.8716 (mtp) cc_final: 0.8497 (mtp) REVERT: N 545 CYS cc_start: 0.7127 (m) cc_final: 0.6851 (m) REVERT: N 675 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7334 (tp30) REVERT: O 213 GLU cc_start: 0.6826 (mp0) cc_final: 0.6574 (mp0) REVERT: R 144 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8713 (ttpt) REVERT: R 205 GLU cc_start: 0.6916 (pp20) cc_final: 0.6501 (pp20) REVERT: T 410 TRP cc_start: 0.8036 (p-90) cc_final: 0.7703 (p-90) REVERT: T 844 ARG cc_start: 0.7930 (ttm170) cc_final: 0.7696 (ttm170) REVERT: U 296 TYR cc_start: 0.8025 (t80) cc_final: 0.7710 (t80) outliers start: 7 outliers final: 3 residues processed: 501 average time/residue: 0.2823 time to fit residues: 226.2084 Evaluate side-chains 460 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 457 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 268 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 0.8980 chunk 414 optimal weight: 0.7980 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 0.0020 chunk 366 optimal weight: 2.9990 chunk 597 optimal weight: 6.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 ASN B 84 ASN B 555 ASN B 638 ASN B 699 ASN C 651 GLN ** C 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 ASN H 154 ASN ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 673 GLN M 721 HIS ** N 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 HIS ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 236 HIS ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 ASN T 431 HIS T 719 HIS U 246 GLN V 108 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054062 restraints weight = 156742.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.055188 restraints weight = 103976.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055394 restraints weight = 78548.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.055873 restraints weight = 64660.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.055886 restraints weight = 58285.463| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 44431 Z= 0.169 Angle : 0.517 7.243 60757 Z= 0.271 Chirality : 0.043 0.177 7098 Planarity : 0.004 0.065 7677 Dihedral : 3.936 50.236 6295 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 0.46 % Allowed : 4.98 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.11), residues: 5849 helix: 1.46 (0.13), residues: 1587 sheet: -0.42 (0.14), residues: 1439 loop : 0.01 (0.12), residues: 2823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG V 36 TYR 0.023 0.001 TYR M 419 PHE 0.027 0.001 PHE O 79 TRP 0.036 0.001 TRP A 521 HIS 0.006 0.001 HIS C 675 Details of bonding type rmsd covalent geometry : bond 0.00376 (44318) covalent geometry : angle 0.50639 (60651) hydrogen bonds : bond 0.04007 ( 1883) hydrogen bonds : angle 5.62574 ( 5307) metal coordination : bond 0.01355 ( 113) metal coordination : angle 2.57499 ( 106) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 466 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 839 MET cc_start: 0.8007 (mmt) cc_final: 0.7793 (mmt) REVERT: C 414 ASP cc_start: 0.8010 (t0) cc_final: 0.7604 (t0) REVERT: C 418 ARG cc_start: 0.7737 (ptt90) cc_final: 0.7527 (ptt180) REVERT: D 704 ASP cc_start: 0.8046 (t0) cc_final: 0.7230 (t0) REVERT: D 741 ASP cc_start: 0.7766 (t0) cc_final: 0.7239 (t70) REVERT: E 27 MET cc_start: 0.7675 (ppp) cc_final: 0.7279 (tmm) REVERT: E 224 ASP cc_start: 0.7816 (t0) cc_final: 0.7188 (t0) REVERT: F 103 TRP cc_start: 0.5331 (m-10) cc_final: 0.5098 (m-90) REVERT: G 106 ARG cc_start: 0.8318 (mmt180) cc_final: 0.8068 (mmt180) REVERT: G 140 ARG cc_start: 0.8227 (ptp90) cc_final: 0.8006 (ptp-110) REVERT: G 201 GLU cc_start: 0.7543 (tt0) cc_final: 0.7082 (tt0) REVERT: H 24 TYR cc_start: 0.7991 (m-80) cc_final: 0.7784 (m-80) REVERT: H 47 GLN cc_start: 0.7338 (mp-120) cc_final: 0.7089 (mp-120) REVERT: H 72 ASN cc_start: 0.7738 (p0) cc_final: 0.7421 (p0) REVERT: H 88 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6696 (mm-30) REVERT: H 196 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6457 (tm-30) REVERT: M 341 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7304 (tt0) REVERT: M 410 ARG cc_start: 0.7121 (tpt170) cc_final: 0.6452 (tpt170) REVERT: M 414 ASP cc_start: 0.7709 (m-30) cc_final: 0.6950 (m-30) REVERT: M 640 MET cc_start: 0.8716 (tmm) cc_final: 0.8202 (tmm) REVERT: M 726 MET cc_start: 0.8763 (mtp) cc_final: 0.8513 (mtp) REVERT: N 868 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7079 (mm-30) REVERT: R 23 TYR cc_start: 0.8143 (t80) cc_final: 0.7762 (t80) REVERT: R 88 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7489 (tm-30) REVERT: R 205 GLU cc_start: 0.7272 (pp20) cc_final: 0.6942 (pp20) REVERT: T 622 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8661 (ttpt) REVERT: T 635 LYS cc_start: 0.8684 (tppt) cc_final: 0.8475 (ptpt) REVERT: T 640 MET cc_start: 0.8559 (mmm) cc_final: 0.8139 (tpp) REVERT: U 296 TYR cc_start: 0.8185 (t80) cc_final: 0.7797 (t80) outliers start: 18 outliers final: 9 residues processed: 471 average time/residue: 0.2923 time to fit residues: 220.0582 Evaluate side-chains 454 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 445 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 110 CYS Chi-restraints excluded: chain L residue 685 LEU Chi-restraints excluded: chain M residue 457 CYS Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain Q residue 301 CYS Chi-restraints excluded: chain U residue 268 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 385 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.0770 chunk 24 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 379 optimal weight: 8.9990 chunk 587 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 520 optimal weight: 0.9980 chunk 463 optimal weight: 6.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 230 ASN G 280 GLN H 6 ASN H 154 ASN M 673 GLN M 721 HIS ** N 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 236 HIS ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 HIS U 246 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.066839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054719 restraints weight = 156083.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.055581 restraints weight = 104740.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055870 restraints weight = 79162.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.056196 restraints weight = 65567.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056266 restraints weight = 60355.611| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 44431 Z= 0.109 Angle : 0.470 7.604 60757 Z= 0.245 Chirality : 0.042 0.151 7098 Planarity : 0.003 0.063 7677 Dihedral : 3.668 32.127 6289 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.09 % Rotamer: Outliers : 0.67 % Allowed : 6.69 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.11), residues: 5849 helix: 1.54 (0.13), residues: 1589 sheet: -0.40 (0.14), residues: 1452 loop : 0.02 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 87 TYR 0.021 0.001 TYR G 309 PHE 0.015 0.001 PHE V 227 TRP 0.043 0.001 TRP B 521 HIS 0.006 0.001 HIS F 125 Details of bonding type rmsd covalent geometry : bond 0.00240 (44318) covalent geometry : angle 0.46070 (60651) hydrogen bonds : bond 0.03375 ( 1883) hydrogen bonds : angle 5.11599 ( 5307) metal coordination : bond 0.00679 ( 113) metal coordination : angle 2.28182 ( 106) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 466 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 414 ASP cc_start: 0.8073 (t0) cc_final: 0.7681 (t0) REVERT: D 741 ASP cc_start: 0.7719 (t0) cc_final: 0.7233 (t70) REVERT: E 224 ASP cc_start: 0.7774 (t0) cc_final: 0.7174 (t0) REVERT: G 106 ARG cc_start: 0.8337 (mmt180) cc_final: 0.8104 (mmt180) REVERT: G 201 GLU cc_start: 0.7424 (tt0) cc_final: 0.6985 (tt0) REVERT: H 38 LYS cc_start: 0.7849 (ptpt) cc_final: 0.7292 (ptpt) REVERT: H 72 ASN cc_start: 0.7728 (p0) cc_final: 0.7364 (p0) REVERT: H 88 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6813 (mm-30) REVERT: M 341 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7431 (tt0) REVERT: M 410 ARG cc_start: 0.7122 (tpt170) cc_final: 0.6580 (tpt170) REVERT: M 414 ASP cc_start: 0.7759 (m-30) cc_final: 0.7222 (m-30) REVERT: M 431 ASP cc_start: 0.7888 (m-30) cc_final: 0.7420 (m-30) REVERT: M 640 MET cc_start: 0.8728 (tmm) cc_final: 0.8235 (tmm) REVERT: M 646 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7249 (mm-30) REVERT: N 679 LYS cc_start: 0.8375 (mttp) cc_final: 0.8024 (mttp) REVERT: N 868 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7016 (mm-30) REVERT: O 2 PHE cc_start: 0.8014 (m-80) cc_final: 0.7724 (m-80) REVERT: R 23 TYR cc_start: 0.8118 (t80) cc_final: 0.7707 (t80) REVERT: R 82 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7960 (ttmm) REVERT: R 88 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7405 (tm-30) REVERT: R 195 LYS cc_start: 0.8537 (ptpp) cc_final: 0.8128 (ptpp) REVERT: R 205 GLU cc_start: 0.7231 (pp20) cc_final: 0.7014 (pp20) REVERT: T 410 TRP cc_start: 0.7894 (p-90) cc_final: 0.7547 (p-90) REVERT: T 575 MET cc_start: 0.7505 (mmm) cc_final: 0.7083 (mmp) REVERT: T 622 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8659 (ttpt) REVERT: U 23 TYR cc_start: 0.8537 (m-80) cc_final: 0.8179 (m-80) REVERT: V 203 ASP cc_start: 0.7825 (t0) cc_final: 0.7505 (t0) REVERT: V 297 TYR cc_start: 0.7882 (m-80) cc_final: 0.7353 (m-80) outliers start: 26 outliers final: 9 residues processed: 474 average time/residue: 0.2767 time to fit residues: 210.0290 Evaluate side-chains 453 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 444 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 110 CYS Chi-restraints excluded: chain L residue 685 LEU Chi-restraints excluded: chain M residue 674 GLU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain Q residue 14 LEU Chi-restraints excluded: chain Q residue 301 CYS Chi-restraints excluded: chain T residue 621 CYS Chi-restraints excluded: chain T residue 679 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 224 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 478 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 651 GLN ** D 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 413 HIS L 431 HIS M 673 GLN M 721 HIS ** N 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 ASN ** U 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.064746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052168 restraints weight = 156489.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.053032 restraints weight = 102492.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053283 restraints weight = 78249.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.053632 restraints weight = 69132.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.053704 restraints weight = 60534.444| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 44431 Z= 0.302 Angle : 0.598 11.486 60757 Z= 0.305 Chirality : 0.045 0.169 7098 Planarity : 0.004 0.057 7677 Dihedral : 4.128 25.381 6287 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 1.08 % Allowed : 8.39 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.11), residues: 5849 helix: 1.22 (0.13), residues: 1591 sheet: -0.66 (0.13), residues: 1494 loop : -0.07 (0.12), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 87 TYR 0.022 0.002 TYR B 695 PHE 0.022 0.002 PHE L 594 TRP 0.035 0.002 TRP A 521 HIS 0.012 0.001 HIS C 675 Details of bonding type rmsd covalent geometry : bond 0.00688 (44318) covalent geometry : angle 0.58130 (60651) hydrogen bonds : bond 0.03856 ( 1883) hydrogen bonds : angle 5.22922 ( 5307) metal coordination : bond 0.02730 ( 113) metal coordination : angle 3.38907 ( 106) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 459 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8134 (mtm) REVERT: C 414 ASP cc_start: 0.8264 (t0) cc_final: 0.7917 (t0) REVERT: D 553 PHE cc_start: 0.7842 (p90) cc_final: 0.7413 (p90) REVERT: D 741 ASP cc_start: 0.7841 (t0) cc_final: 0.7257 (t70) REVERT: D 747 MET cc_start: 0.8420 (mmm) cc_final: 0.8219 (mmm) REVERT: E 27 MET cc_start: 0.7875 (ppp) cc_final: 0.7627 (ppp) REVERT: E 224 ASP cc_start: 0.7840 (t0) cc_final: 0.7346 (t0) REVERT: F 103 TRP cc_start: 0.5877 (m-10) cc_final: 0.5261 (m-90) REVERT: G 201 GLU cc_start: 0.7591 (tt0) cc_final: 0.7085 (tt0) REVERT: H 70 TYR cc_start: 0.7892 (m-10) cc_final: 0.7581 (m-10) REVERT: H 72 ASN cc_start: 0.7867 (p0) cc_final: 0.7549 (p0) REVERT: H 196 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6812 (tm-30) REVERT: M 410 ARG cc_start: 0.7124 (tpt170) cc_final: 0.6538 (tpt170) REVERT: M 414 ASP cc_start: 0.7710 (m-30) cc_final: 0.7136 (m-30) REVERT: M 431 ASP cc_start: 0.7959 (m-30) cc_final: 0.7351 (m-30) REVERT: M 640 MET cc_start: 0.8620 (tmm) cc_final: 0.8155 (tmm) REVERT: M 646 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7280 (mm-30) REVERT: M 726 MET cc_start: 0.8879 (mtp) cc_final: 0.8648 (mtp) REVERT: N 646 LYS cc_start: 0.8444 (mmmm) cc_final: 0.8018 (mmmm) REVERT: N 868 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7179 (mm-30) REVERT: O 167 CYS cc_start: 0.7620 (p) cc_final: 0.7351 (p) REVERT: R 88 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7571 (tm-30) REVERT: R 195 LYS cc_start: 0.8541 (ptpp) cc_final: 0.8106 (ptpp) REVERT: R 205 GLU cc_start: 0.7536 (pp20) cc_final: 0.7296 (pp20) REVERT: T 410 TRP cc_start: 0.8129 (p-90) cc_final: 0.7659 (p-90) REVERT: T 575 MET cc_start: 0.7726 (mmm) cc_final: 0.7303 (mmp) REVERT: T 622 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8642 (ttpt) REVERT: V 297 TYR cc_start: 0.8165 (m-80) cc_final: 0.7667 (m-80) outliers start: 42 outliers final: 25 residues processed: 482 average time/residue: 0.2739 time to fit residues: 213.2968 Evaluate side-chains 464 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 438 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain D residue 852 ASP Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain H residue 110 CYS Chi-restraints excluded: chain H residue 153 CYS Chi-restraints excluded: chain L residue 685 LEU Chi-restraints excluded: chain L residue 828 HIS Chi-restraints excluded: chain M residue 457 CYS Chi-restraints excluded: chain M residue 674 GLU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 669 ASN Chi-restraints excluded: chain N residue 742 VAL Chi-restraints excluded: chain N residue 888 CYS Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 270 ILE Chi-restraints excluded: chain Q residue 231 LEU Chi-restraints excluded: chain Q residue 301 CYS Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain T residue 679 MET Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 515 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 481 optimal weight: 7.9990 chunk 276 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 270 optimal weight: 0.8980 chunk 563 optimal weight: 0.8980 chunk 304 optimal weight: 0.5980 chunk 511 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN ** D 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 721 HIS ** N 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN O 102 HIS ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 152 GLN R 107 ASN ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.065489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052952 restraints weight = 156055.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.053945 restraints weight = 108179.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054402 restraints weight = 76161.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054811 restraints weight = 62902.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054851 restraints weight = 57482.113| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 44431 Z= 0.177 Angle : 0.519 9.566 60757 Z= 0.266 Chirality : 0.043 0.153 7098 Planarity : 0.003 0.056 7677 Dihedral : 3.964 24.649 6287 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.28 % Favored : 96.70 % Rotamer: Outliers : 1.16 % Allowed : 9.45 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.11), residues: 5849 helix: 1.30 (0.13), residues: 1587 sheet: -0.72 (0.13), residues: 1488 loop : -0.05 (0.12), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 36 TYR 0.031 0.001 TYR B 695 PHE 0.019 0.001 PHE M 400 TRP 0.034 0.001 TRP A 521 HIS 0.007 0.001 HIS M 721 Details of bonding type rmsd covalent geometry : bond 0.00402 (44318) covalent geometry : angle 0.50552 (60651) hydrogen bonds : bond 0.03300 ( 1883) hydrogen bonds : angle 5.00253 ( 5307) metal coordination : bond 0.01394 ( 113) metal coordination : angle 2.89487 ( 106) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 455 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8126 (mtm) REVERT: A 640 MET cc_start: 0.7568 (mmm) cc_final: 0.7330 (mmm) REVERT: C 414 ASP cc_start: 0.8114 (t0) cc_final: 0.7483 (t0) REVERT: D 553 PHE cc_start: 0.7808 (p90) cc_final: 0.7536 (p90) REVERT: D 741 ASP cc_start: 0.7774 (t0) cc_final: 0.7244 (t70) REVERT: E 224 ASP cc_start: 0.7735 (t0) cc_final: 0.7274 (t0) REVERT: F 103 TRP cc_start: 0.5435 (m-10) cc_final: 0.4919 (m-90) REVERT: G 201 GLU cc_start: 0.7473 (tt0) cc_final: 0.7016 (tt0) REVERT: H 72 ASN cc_start: 0.7887 (p0) cc_final: 0.7580 (p0) REVERT: H 88 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6824 (mm-30) REVERT: H 196 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6791 (tm-30) REVERT: M 410 ARG cc_start: 0.7141 (tpt170) cc_final: 0.6539 (tpt170) REVERT: M 414 ASP cc_start: 0.7742 (m-30) cc_final: 0.7126 (m-30) REVERT: M 431 ASP cc_start: 0.7968 (m-30) cc_final: 0.7286 (m-30) REVERT: M 640 MET cc_start: 0.8643 (tmm) cc_final: 0.8204 (tmm) REVERT: M 646 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7257 (mm-30) REVERT: N 646 LYS cc_start: 0.8476 (mmmm) cc_final: 0.8194 (mmmm) REVERT: N 857 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7702 (tp40) REVERT: N 868 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7133 (mm-30) REVERT: O 167 CYS cc_start: 0.7573 (p) cc_final: 0.7313 (p) REVERT: Q 203 ASN cc_start: 0.8424 (t0) cc_final: 0.8215 (t0) REVERT: R 23 TYR cc_start: 0.8065 (t80) cc_final: 0.7569 (t80) REVERT: R 88 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7528 (tm-30) REVERT: R 195 LYS cc_start: 0.8553 (ptpp) cc_final: 0.8127 (ptpp) REVERT: T 410 TRP cc_start: 0.8080 (p-90) cc_final: 0.7652 (p-90) REVERT: T 575 MET cc_start: 0.7614 (mmm) cc_final: 0.7238 (mmp) REVERT: T 622 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8674 (ttpp) outliers start: 45 outliers final: 26 residues processed: 479 average time/residue: 0.2758 time to fit residues: 212.9043 Evaluate side-chains 465 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 438 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 345 TYR Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 852 ASP Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain H residue 110 CYS Chi-restraints excluded: chain H residue 153 CYS Chi-restraints excluded: chain L residue 483 ILE Chi-restraints excluded: chain L residue 685 LEU Chi-restraints excluded: chain L residue 828 HIS Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 457 CYS Chi-restraints excluded: chain M residue 674 GLU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 669 ASN Chi-restraints excluded: chain N residue 742 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 270 ILE Chi-restraints excluded: chain Q residue 301 CYS Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain T residue 679 MET Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 103 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 555 optimal weight: 0.8980 chunk 284 optimal weight: 2.9990 chunk 347 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 291 optimal weight: 0.5980 chunk 210 optimal weight: 40.0000 chunk 314 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 HIS ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 721 HIS M 767 GLN ** N 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 152 GLN R 107 ASN ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.066126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054044 restraints weight = 156173.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054986 restraints weight = 104467.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.055303 restraints weight = 77987.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.055574 restraints weight = 64566.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055644 restraints weight = 59778.911| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 44431 Z= 0.118 Angle : 0.487 8.226 60757 Z= 0.251 Chirality : 0.042 0.154 7098 Planarity : 0.003 0.056 7677 Dihedral : 3.796 23.750 6287 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 0.96 % Allowed : 10.33 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.11), residues: 5849 helix: 1.43 (0.13), residues: 1586 sheet: -0.63 (0.13), residues: 1487 loop : 0.01 (0.13), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 87 TYR 0.030 0.001 TYR B 695 PHE 0.031 0.001 PHE O 79 TRP 0.040 0.001 TRP A 521 HIS 0.007 0.001 HIS M 721 Details of bonding type rmsd covalent geometry : bond 0.00265 (44318) covalent geometry : angle 0.47592 (60651) hydrogen bonds : bond 0.03008 ( 1883) hydrogen bonds : angle 4.79131 ( 5307) metal coordination : bond 0.00830 ( 113) metal coordination : angle 2.56679 ( 106) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 460 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 353 PHE cc_start: 0.6960 (t80) cc_final: 0.6692 (t80) REVERT: C 414 ASP cc_start: 0.7981 (t0) cc_final: 0.7391 (t0) REVERT: C 742 MET cc_start: 0.7076 (mmm) cc_final: 0.6663 (tpp) REVERT: D 553 PHE cc_start: 0.7795 (p90) cc_final: 0.7528 (p90) REVERT: D 741 ASP cc_start: 0.7657 (t0) cc_final: 0.7259 (t70) REVERT: E 224 ASP cc_start: 0.7675 (t0) cc_final: 0.7205 (t0) REVERT: G 201 GLU cc_start: 0.7385 (tt0) cc_final: 0.7056 (tt0) REVERT: H 70 TYR cc_start: 0.7975 (m-80) cc_final: 0.7771 (m-10) REVERT: H 72 ASN cc_start: 0.7845 (p0) cc_final: 0.7523 (p0) REVERT: H 88 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6861 (mm-30) REVERT: H 196 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6853 (tm-30) REVERT: M 410 ARG cc_start: 0.7127 (tpt170) cc_final: 0.6485 (tpt170) REVERT: M 414 ASP cc_start: 0.7719 (m-30) cc_final: 0.7084 (m-30) REVERT: M 431 ASP cc_start: 0.7950 (m-30) cc_final: 0.7280 (m-30) REVERT: M 640 MET cc_start: 0.8679 (tmm) cc_final: 0.8214 (tmm) REVERT: N 646 LYS cc_start: 0.8515 (mmmm) cc_final: 0.8241 (mmmm) REVERT: N 679 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8160 (mttp) REVERT: N 857 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7691 (tp40) REVERT: N 868 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7059 (mm-30) REVERT: O 167 CYS cc_start: 0.7582 (p) cc_final: 0.7267 (p) REVERT: O 198 GLN cc_start: 0.7804 (mp10) cc_final: 0.7599 (mp10) REVERT: R 23 TYR cc_start: 0.8037 (t80) cc_final: 0.7521 (t80) REVERT: R 88 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7486 (tm-30) REVERT: T 410 TRP cc_start: 0.7999 (p-90) cc_final: 0.7629 (p-90) REVERT: T 413 HIS cc_start: 0.7577 (p-80) cc_final: 0.7139 (p-80) REVERT: T 575 MET cc_start: 0.7587 (mmm) cc_final: 0.7239 (mmp) REVERT: T 622 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8663 (ttpp) REVERT: T 635 LYS cc_start: 0.8726 (tppt) cc_final: 0.8521 (tmtt) REVERT: V 36 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.8024 (mmt-90) outliers start: 37 outliers final: 22 residues processed: 477 average time/residue: 0.2815 time to fit residues: 215.3690 Evaluate side-chains 468 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 446 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 345 TYR Chi-restraints excluded: chain C residue 419 TYR Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 852 ASP Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 110 CYS Chi-restraints excluded: chain H residue 153 CYS Chi-restraints excluded: chain L residue 685 LEU Chi-restraints excluded: chain L residue 828 HIS Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 457 CYS Chi-restraints excluded: chain M residue 674 GLU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 669 ASN Chi-restraints excluded: chain N residue 742 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain Q residue 301 CYS Chi-restraints excluded: chain T residue 679 MET Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 593 optimal weight: 3.9990 chunk 210 optimal weight: 40.0000 chunk 282 optimal weight: 1.9990 chunk 544 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 465 optimal weight: 7.9990 chunk 526 optimal weight: 7.9990 chunk 239 optimal weight: 0.8980 chunk 199 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 HIS ** G 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 721 HIS ** N 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.064014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.051851 restraints weight = 156470.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052531 restraints weight = 101690.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.052783 restraints weight = 81915.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.052998 restraints weight = 68339.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.053492 restraints weight = 62943.960| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.155 44431 Z= 0.387 Angle : 0.665 15.387 60757 Z= 0.336 Chirality : 0.047 0.175 7098 Planarity : 0.004 0.054 7677 Dihedral : 4.343 25.173 6287 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.80 % Favored : 95.18 % Rotamer: Outliers : 1.37 % Allowed : 10.95 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.11), residues: 5849 helix: 1.01 (0.13), residues: 1595 sheet: -0.89 (0.13), residues: 1507 loop : -0.17 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 87 TYR 0.028 0.002 TYR B 695 PHE 0.026 0.003 PHE O 79 TRP 0.030 0.002 TRP T 128 HIS 0.013 0.002 HIS C 675 Details of bonding type rmsd covalent geometry : bond 0.00881 (44318) covalent geometry : angle 0.64387 (60651) hydrogen bonds : bond 0.03891 ( 1883) hydrogen bonds : angle 5.24133 ( 5307) metal coordination : bond 0.03358 ( 113) metal coordination : angle 4.06072 ( 106) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 445 time to evaluate : 1.794 Fit side-chains revert: symmetry clash REVERT: B 521 TRP cc_start: 0.7437 (m-10) cc_final: 0.7123 (m-10) REVERT: C 353 PHE cc_start: 0.7249 (t80) cc_final: 0.6896 (t80) REVERT: D 553 PHE cc_start: 0.7854 (p90) cc_final: 0.7581 (p90) REVERT: D 741 ASP cc_start: 0.7775 (t0) cc_final: 0.7427 (t70) REVERT: D 868 GLU cc_start: 0.7484 (tp30) cc_final: 0.7245 (tp30) REVERT: D 869 ILE cc_start: 0.8207 (mm) cc_final: 0.7958 (mm) REVERT: E 224 ASP cc_start: 0.7752 (t0) cc_final: 0.7313 (t0) REVERT: F 282 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.6964 (t60) REVERT: G 201 GLU cc_start: 0.7590 (tt0) cc_final: 0.7227 (tt0) REVERT: H 38 LYS cc_start: 0.7977 (ptpt) cc_final: 0.7432 (ptpt) REVERT: H 70 TYR cc_start: 0.8087 (m-80) cc_final: 0.7773 (m-10) REVERT: H 72 ASN cc_start: 0.7870 (p0) cc_final: 0.7507 (p0) REVERT: H 88 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6863 (mm-30) REVERT: M 410 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6552 (tpt170) REVERT: M 414 ASP cc_start: 0.7705 (m-30) cc_final: 0.7099 (m-30) REVERT: M 431 ASP cc_start: 0.8033 (m-30) cc_final: 0.7279 (m-30) REVERT: N 646 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8141 (mmmm) REVERT: N 675 GLU cc_start: 0.7779 (tp30) cc_final: 0.7563 (tp30) REVERT: N 868 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7220 (mm-30) REVERT: O 167 CYS cc_start: 0.7521 (p) cc_final: 0.7176 (p) REVERT: R 88 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7598 (tm-30) REVERT: T 410 TRP cc_start: 0.8227 (p-90) cc_final: 0.7838 (p-90) REVERT: U 267 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7883 (mtp85) outliers start: 53 outliers final: 37 residues processed: 479 average time/residue: 0.2844 time to fit residues: 219.3280 Evaluate side-chains 468 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 429 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 345 TYR Chi-restraints excluded: chain C residue 419 TYR Chi-restraints excluded: chain D residue 852 ASP Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 282 TRP Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain H residue 110 CYS Chi-restraints excluded: chain H residue 153 CYS Chi-restraints excluded: chain L residue 685 LEU Chi-restraints excluded: chain L residue 828 HIS Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 457 CYS Chi-restraints excluded: chain M residue 674 GLU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 669 ASN Chi-restraints excluded: chain N residue 742 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 270 ILE Chi-restraints excluded: chain Q residue 231 LEU Chi-restraints excluded: chain Q residue 270 ILE Chi-restraints excluded: chain Q residue 301 CYS Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain T residue 679 MET Chi-restraints excluded: chain T residue 861 LEU Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 305 HIS Chi-restraints excluded: chain V residue 238 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 421 optimal weight: 0.0470 chunk 254 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 193 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 592 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 56 HIS G 236 HIS ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 721 HIS ** N 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 152 GLN ** T 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 472 HIS ** U 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.065934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.053759 restraints weight = 155951.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054740 restraints weight = 108100.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.055047 restraints weight = 78773.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.055349 restraints weight = 64662.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.055428 restraints weight = 59447.128| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 44431 Z= 0.112 Angle : 0.516 10.966 60757 Z= 0.263 Chirality : 0.042 0.146 7098 Planarity : 0.003 0.077 7677 Dihedral : 3.955 24.393 6287 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.15 % Favored : 96.84 % Rotamer: Outliers : 0.90 % Allowed : 11.95 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.11), residues: 5849 helix: 1.31 (0.13), residues: 1600 sheet: -0.78 (0.13), residues: 1514 loop : -0.03 (0.13), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 411 TYR 0.030 0.001 TYR M 419 PHE 0.033 0.001 PHE O 79 TRP 0.046 0.001 TRP A 521 HIS 0.012 0.001 HIS G 277 Details of bonding type rmsd covalent geometry : bond 0.00247 (44318) covalent geometry : angle 0.50252 (60651) hydrogen bonds : bond 0.03017 ( 1883) hydrogen bonds : angle 4.84680 ( 5307) metal coordination : bond 0.00723 ( 113) metal coordination : angle 2.89009 ( 106) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 453 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 521 TRP cc_start: 0.7350 (m-10) cc_final: 0.7140 (m-10) REVERT: B 844 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.7799 (ptp90) REVERT: C 353 PHE cc_start: 0.7102 (t80) cc_final: 0.6868 (t80) REVERT: C 414 ASP cc_start: 0.8111 (t0) cc_final: 0.7482 (t0) REVERT: D 553 PHE cc_start: 0.7786 (p90) cc_final: 0.7542 (p90) REVERT: D 741 ASP cc_start: 0.7676 (t0) cc_final: 0.7345 (t70) REVERT: D 868 GLU cc_start: 0.7520 (tp30) cc_final: 0.7245 (tp30) REVERT: E 27 MET cc_start: 0.6806 (ppp) cc_final: 0.6422 (ttt) REVERT: E 224 ASP cc_start: 0.7631 (t0) cc_final: 0.7146 (t0) REVERT: F 282 TRP cc_start: 0.7792 (OUTLIER) cc_final: 0.6890 (t60) REVERT: F 286 TRP cc_start: 0.7788 (m100) cc_final: 0.7239 (m100) REVERT: G 201 GLU cc_start: 0.7431 (tt0) cc_final: 0.7090 (tt0) REVERT: H 70 TYR cc_start: 0.8045 (m-80) cc_final: 0.7817 (m-10) REVERT: H 72 ASN cc_start: 0.7858 (p0) cc_final: 0.7514 (p0) REVERT: H 88 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6743 (mm-30) REVERT: H 122 CYS cc_start: 0.8166 (m) cc_final: 0.7558 (m) REVERT: M 410 ARG cc_start: 0.7174 (tpt170) cc_final: 0.6500 (tpt170) REVERT: M 414 ASP cc_start: 0.7723 (m-30) cc_final: 0.7081 (m-30) REVERT: M 431 ASP cc_start: 0.7992 (m-30) cc_final: 0.7201 (m-30) REVERT: M 640 MET cc_start: 0.8648 (tmm) cc_final: 0.8202 (tmm) REVERT: N 646 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8120 (mmmm) REVERT: N 857 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7674 (tp40) REVERT: N 868 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7082 (mm-30) REVERT: O 2 PHE cc_start: 0.7821 (m-80) cc_final: 0.7565 (m-80) REVERT: O 167 CYS cc_start: 0.7548 (p) cc_final: 0.7211 (p) REVERT: O 240 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8661 (mm) REVERT: R 23 TYR cc_start: 0.7991 (t80) cc_final: 0.7425 (t80) REVERT: R 87 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7988 (ttm110) REVERT: R 88 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7518 (tm-30) REVERT: T 635 LYS cc_start: 0.8744 (tppt) cc_final: 0.8450 (tppt) REVERT: U 267 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7650 (mtp85) REVERT: V 36 ARG cc_start: 0.8370 (mmt-90) cc_final: 0.8092 (mmt-90) REVERT: V 297 TYR cc_start: 0.7926 (m-80) cc_final: 0.7457 (m-80) outliers start: 35 outliers final: 23 residues processed: 473 average time/residue: 0.2909 time to fit residues: 220.9659 Evaluate side-chains 465 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 439 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 345 TYR Chi-restraints excluded: chain C residue 419 TYR Chi-restraints excluded: chain C residue 644 TYR Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 740 ARG Chi-restraints excluded: chain D residue 852 ASP Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 282 TRP Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain H residue 110 CYS Chi-restraints excluded: chain L residue 685 LEU Chi-restraints excluded: chain L residue 828 HIS Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 457 CYS Chi-restraints excluded: chain N residue 669 ASN Chi-restraints excluded: chain N residue 742 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain Q residue 301 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain T residue 679 MET Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 182 optimal weight: 7.9990 chunk 318 optimal weight: 1.9990 chunk 414 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 338 optimal weight: 4.9990 chunk 545 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 586 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 585 optimal weight: 3.9990 chunk 567 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 HIS ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 721 HIS ** N 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 152 GLN R 107 ASN ** T 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 472 HIS ** U 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053176 restraints weight = 155691.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054210 restraints weight = 101063.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.054350 restraints weight = 77151.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054535 restraints weight = 67389.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.054981 restraints weight = 61423.850| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 44431 Z= 0.167 Angle : 0.535 10.776 60757 Z= 0.271 Chirality : 0.043 0.177 7098 Planarity : 0.004 0.090 7677 Dihedral : 3.924 24.226 6287 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 1.06 % Allowed : 11.90 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.11), residues: 5849 helix: 1.35 (0.13), residues: 1598 sheet: -0.76 (0.13), residues: 1510 loop : -0.01 (0.13), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 411 TYR 0.034 0.001 TYR M 419 PHE 0.033 0.001 PHE O 79 TRP 0.039 0.001 TRP A 521 HIS 0.019 0.001 HIS T 413 Details of bonding type rmsd covalent geometry : bond 0.00382 (44318) covalent geometry : angle 0.52152 (60651) hydrogen bonds : bond 0.03126 ( 1883) hydrogen bonds : angle 4.80111 ( 5307) metal coordination : bond 0.01391 ( 113) metal coordination : angle 2.90708 ( 106) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 442 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 521 TRP cc_start: 0.7363 (m-10) cc_final: 0.7142 (m-10) REVERT: B 844 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.7802 (ptp90) REVERT: C 353 PHE cc_start: 0.7139 (t80) cc_final: 0.6938 (t80) REVERT: C 414 ASP cc_start: 0.8055 (t0) cc_final: 0.7391 (t0) REVERT: D 553 PHE cc_start: 0.7814 (p90) cc_final: 0.7538 (p90) REVERT: D 741 ASP cc_start: 0.7655 (t0) cc_final: 0.7260 (t70) REVERT: D 868 GLU cc_start: 0.7448 (tp30) cc_final: 0.7147 (tp30) REVERT: E 27 MET cc_start: 0.7031 (ppp) cc_final: 0.6621 (tmm) REVERT: E 224 ASP cc_start: 0.7649 (t0) cc_final: 0.7190 (t0) REVERT: F 282 TRP cc_start: 0.7815 (OUTLIER) cc_final: 0.6913 (t60) REVERT: G 201 GLU cc_start: 0.7491 (tt0) cc_final: 0.7101 (tt0) REVERT: H 38 LYS cc_start: 0.7960 (ptpt) cc_final: 0.7409 (ptpt) REVERT: H 70 TYR cc_start: 0.8054 (m-80) cc_final: 0.7804 (m-10) REVERT: H 72 ASN cc_start: 0.7873 (p0) cc_final: 0.7527 (p0) REVERT: H 88 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6748 (mm-30) REVERT: H 122 CYS cc_start: 0.8166 (m) cc_final: 0.7575 (m) REVERT: M 410 ARG cc_start: 0.7175 (tpt170) cc_final: 0.6496 (tpt170) REVERT: M 414 ASP cc_start: 0.7729 (m-30) cc_final: 0.7063 (m-30) REVERT: M 431 ASP cc_start: 0.8033 (m-30) cc_final: 0.7226 (m-30) REVERT: M 640 MET cc_start: 0.8644 (tmm) cc_final: 0.8209 (tmm) REVERT: N 646 LYS cc_start: 0.8611 (mmmm) cc_final: 0.8259 (mmmm) REVERT: N 857 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7718 (tp40) REVERT: N 868 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7080 (mm-30) REVERT: O 167 CYS cc_start: 0.7610 (p) cc_final: 0.7277 (p) REVERT: R 23 TYR cc_start: 0.7984 (t80) cc_final: 0.7417 (t80) REVERT: R 88 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7533 (tm-30) REVERT: R 144 LYS cc_start: 0.8993 (ttmm) cc_final: 0.8790 (ttpt) REVERT: T 635 LYS cc_start: 0.8778 (tppt) cc_final: 0.8477 (tppt) REVERT: U 267 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7610 (mtp85) REVERT: V 36 ARG cc_start: 0.8381 (mmt-90) cc_final: 0.8093 (mmt-90) outliers start: 41 outliers final: 28 residues processed: 467 average time/residue: 0.2799 time to fit residues: 209.6906 Evaluate side-chains 467 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 437 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 345 TYR Chi-restraints excluded: chain C residue 419 TYR Chi-restraints excluded: chain C residue 644 TYR Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 852 ASP Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 282 TRP Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 110 CYS Chi-restraints excluded: chain L residue 377 CYS Chi-restraints excluded: chain L residue 685 LEU Chi-restraints excluded: chain L residue 828 HIS Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 457 CYS Chi-restraints excluded: chain N residue 669 ASN Chi-restraints excluded: chain N residue 742 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain Q residue 231 LEU Chi-restraints excluded: chain Q residue 301 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain T residue 622 LYS Chi-restraints excluded: chain T residue 679 MET Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 499 optimal weight: 9.9990 chunk 588 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 592 optimal weight: 3.9990 chunk 518 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 178 HIS ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 GLN M 721 HIS ** N 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS Q 152 GLN R 107 ASN ** T 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 472 HIS ** U 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.065063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052937 restraints weight = 156131.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.054003 restraints weight = 98698.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.054163 restraints weight = 74770.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054422 restraints weight = 64133.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054526 restraints weight = 58262.646| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 44431 Z= 0.223 Angle : 0.573 14.412 60757 Z= 0.289 Chirality : 0.044 0.183 7098 Planarity : 0.004 0.072 7677 Dihedral : 4.040 23.696 6287 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.14 % Rotamer: Outliers : 1.01 % Allowed : 12.19 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.11), residues: 5849 helix: 1.28 (0.13), residues: 1601 sheet: -0.79 (0.13), residues: 1508 loop : -0.06 (0.13), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 87 TYR 0.035 0.002 TYR M 419 PHE 0.031 0.002 PHE O 79 TRP 0.038 0.001 TRP A 521 HIS 0.017 0.001 HIS T 413 Details of bonding type rmsd covalent geometry : bond 0.00511 (44318) covalent geometry : angle 0.55785 (60651) hydrogen bonds : bond 0.03287 ( 1883) hydrogen bonds : angle 4.89220 ( 5307) metal coordination : bond 0.01896 ( 113) metal coordination : angle 3.13543 ( 106) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 440 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7939 (mmt-90) REVERT: B 521 TRP cc_start: 0.7371 (m-10) cc_final: 0.7150 (m-10) REVERT: B 844 ARG cc_start: 0.8501 (ttp-110) cc_final: 0.7802 (ptp90) REVERT: C 414 ASP cc_start: 0.8050 (t0) cc_final: 0.7670 (t0) REVERT: D 553 PHE cc_start: 0.7826 (p90) cc_final: 0.7558 (p90) REVERT: D 741 ASP cc_start: 0.7694 (t0) cc_final: 0.7366 (t70) REVERT: D 868 GLU cc_start: 0.7479 (tp30) cc_final: 0.7159 (tp30) REVERT: E 27 MET cc_start: 0.6996 (ppp) cc_final: 0.6655 (tmm) REVERT: E 224 ASP cc_start: 0.7674 (t0) cc_final: 0.7228 (t0) REVERT: F 282 TRP cc_start: 0.7852 (OUTLIER) cc_final: 0.6979 (t60) REVERT: F 286 TRP cc_start: 0.7836 (m100) cc_final: 0.7355 (m100) REVERT: G 201 GLU cc_start: 0.7427 (tt0) cc_final: 0.7048 (tt0) REVERT: H 38 LYS cc_start: 0.8004 (ptpt) cc_final: 0.7451 (ptpt) REVERT: H 70 TYR cc_start: 0.8059 (m-80) cc_final: 0.7612 (m-10) REVERT: H 72 ASN cc_start: 0.7865 (p0) cc_final: 0.7517 (p0) REVERT: H 88 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6809 (mm-30) REVERT: H 122 CYS cc_start: 0.8157 (m) cc_final: 0.7566 (m) REVERT: M 410 ARG cc_start: 0.7227 (tpt170) cc_final: 0.6540 (tpt170) REVERT: M 414 ASP cc_start: 0.7698 (m-30) cc_final: 0.7068 (m-30) REVERT: M 428 GLU cc_start: 0.8109 (pm20) cc_final: 0.7680 (pm20) REVERT: M 431 ASP cc_start: 0.8034 (m-30) cc_final: 0.7228 (m-30) REVERT: M 640 MET cc_start: 0.8650 (tmm) cc_final: 0.8196 (tmm) REVERT: N 646 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8198 (mmmm) REVERT: N 857 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7735 (tp40) REVERT: N 868 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7197 (mm-30) REVERT: O 167 CYS cc_start: 0.7611 (p) cc_final: 0.7282 (p) REVERT: R 88 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7542 (tm-30) REVERT: T 410 TRP cc_start: 0.8120 (p-90) cc_final: 0.7722 (p-90) REVERT: T 424 LYS cc_start: 0.8409 (tppt) cc_final: 0.7954 (mmmt) REVERT: T 635 LYS cc_start: 0.8771 (tppt) cc_final: 0.8511 (tppt) REVERT: T 640 MET cc_start: 0.8378 (mmm) cc_final: 0.8175 (mmm) REVERT: U 267 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7722 (mtp85) REVERT: V 36 ARG cc_start: 0.8379 (mmt-90) cc_final: 0.8015 (mmt-90) outliers start: 39 outliers final: 32 residues processed: 463 average time/residue: 0.2876 time to fit residues: 213.8318 Evaluate side-chains 470 residues out of total 5291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 436 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 345 TYR Chi-restraints excluded: chain C residue 419 TYR Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 852 ASP Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 282 TRP Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 110 CYS Chi-restraints excluded: chain H residue 153 CYS Chi-restraints excluded: chain L residue 377 CYS Chi-restraints excluded: chain L residue 685 LEU Chi-restraints excluded: chain L residue 828 HIS Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 457 CYS Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 669 ASN Chi-restraints excluded: chain N residue 742 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 270 ILE Chi-restraints excluded: chain Q residue 231 LEU Chi-restraints excluded: chain Q residue 301 CYS Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain T residue 605 VAL Chi-restraints excluded: chain T residue 622 LYS Chi-restraints excluded: chain T residue 679 MET Chi-restraints excluded: chain T residue 861 LEU Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 317 optimal weight: 0.6980 chunk 523 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 562 optimal weight: 0.9980 chunk 229 optimal weight: 6.9990 chunk 494 optimal weight: 4.9990 chunk 528 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 349 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 721 HIS ** N 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS Q 152 GLN ** T 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 472 HIS ** U 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052937 restraints weight = 156524.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053849 restraints weight = 108033.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054256 restraints weight = 78038.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054432 restraints weight = 67535.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054593 restraints weight = 60536.014| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 44431 Z= 0.182 Angle : 0.548 10.591 60757 Z= 0.278 Chirality : 0.043 0.156 7098 Planarity : 0.004 0.062 7677 Dihedral : 3.980 22.202 6287 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.22 % Rotamer: Outliers : 1.01 % Allowed : 12.29 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.11), residues: 5849 helix: 1.31 (0.13), residues: 1599 sheet: -0.78 (0.13), residues: 1517 loop : -0.03 (0.13), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 87 TYR 0.034 0.001 TYR M 419 PHE 0.032 0.001 PHE O 79 TRP 0.037 0.001 TRP A 521 HIS 0.014 0.001 HIS T 413 Details of bonding type rmsd covalent geometry : bond 0.00418 (44318) covalent geometry : angle 0.53430 (60651) hydrogen bonds : bond 0.03148 ( 1883) hydrogen bonds : angle 4.83332 ( 5307) metal coordination : bond 0.01448 ( 113) metal coordination : angle 2.99858 ( 106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7613.44 seconds wall clock time: 132 minutes 39.35 seconds (7959.35 seconds total)