Starting phenix.real_space_refine on Mon Mar 18 11:20:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvw_16274/03_2024/8bvw_16274_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvw_16274/03_2024/8bvw_16274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvw_16274/03_2024/8bvw_16274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvw_16274/03_2024/8bvw_16274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvw_16274/03_2024/8bvw_16274_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvw_16274/03_2024/8bvw_16274_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 17 6.06 5 P 410 5.49 5 Mg 1 5.21 5 S 438 5.16 5 C 52414 2.51 5 N 14973 2.21 5 O 16526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 252": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 84783 Number of models: 1 Model: "" Number of chains: 54 Chain: "0" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4890 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Chain: "1" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5751 Classifications: {'peptide': 714} Link IDs: {'PTRANS': 32, 'TRANS': 681} Chain breaks: 1 Chain: "2" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2167 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 5 Chain: "3" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3337 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 399} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "4" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 2 Chain: "5" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2066 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 1 Chain: "6" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 548 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "7" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1724 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "8" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2378 Classifications: {'peptide': 299} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 280} Chain: "9" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 271} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 11274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11274 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 9076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9076 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1953 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 1 Chain: "N" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 4213 Classifications: {'DNA': 206} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 205} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 4227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 4227 Classifications: {'DNA': 206} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 205} Chain: "U" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "W" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1659 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 1 Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 2, 'TRANS': 16} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "a" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "c" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "d" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "e" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "f" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "g" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "h" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "1" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "4" 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: "5" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6431 SG CYS 1 190 127.736 204.980 114.568 1.00 58.83 S ATOM 5833 SG CYS 1 116 129.956 199.050 117.462 1.00 53.61 S ATOM 5973 SG CYS 1 134 125.312 201.858 119.743 1.00 61.53 S ATOM 6142 SG CYS 1 155 129.894 205.757 117.189 1.00 64.75 S ATOM 18555 SG CYS 4 345 131.498 139.764 62.087 1.00 56.59 S ATOM 18577 SG CYS 4 348 131.697 136.270 63.554 1.00 61.50 S ATOM 18734 SG CYS 4 368 130.358 139.256 65.669 1.00 62.59 S ATOM 18755 SG CYS 4 371 133.895 139.138 64.904 1.00 63.99 S ATOM 18675 SG CYS 4 360 135.943 148.083 60.577 1.00 56.94 S ATOM 18842 SG CYS 4 382 138.872 147.861 60.921 1.00 58.57 S ATOM 18119 SG CYS 4 291 173.795 146.722 82.883 1.00 57.30 S ATOM 18141 SG CYS 4 294 173.868 146.104 86.433 1.00 56.36 S ATOM 18230 SG CYS 4 305 170.954 147.840 84.996 1.00 50.76 S ATOM 18253 SG CYS 4 308 174.607 149.429 85.844 1.00 49.46 S ATOM 20764 SG CYS 5 268 159.405 160.013 74.243 1.00 59.54 S ATOM 20783 SG CYS 5 271 157.355 161.427 71.943 1.00 56.93 S ATOM 20868 SG CYS 5 282 159.224 163.811 71.719 1.00 63.48 S ATOM 20822 SG CYS 5 276 172.060 157.615 68.079 1.00 64.24 S ATOM 21534 SG CYS 7 6 112.893 193.432 167.862 1.00 49.66 S ATOM 21751 SG CYS 7 34 111.388 194.417 171.522 1.00 61.98 S ATOM 21695 SG CYS 7 26 108.294 204.140 166.735 1.00 47.97 S ATOM 28391 SG CYS A 71 102.494 177.238 210.892 1.00 34.86 S ATOM 28413 SG CYS A 74 99.731 175.392 209.003 1.00 36.51 S ATOM 28460 SG CYS A 81 101.909 173.657 211.513 1.00 40.62 S ATOM 28695 SG CYS A 111 113.239 150.930 171.384 1.00 56.14 S ATOM 28723 SG CYS A 114 111.003 152.814 170.036 1.00 54.28 S ATOM 29036 SG CYS A 154 112.261 149.884 167.760 1.00 50.52 S ATOM 47846 SG CYS B1119 92.238 169.497 196.528 1.00 42.81 S ATOM 47868 SG CYS B1122 95.618 167.604 196.419 1.00 43.44 S ATOM 47983 SG CYS B1137 95.343 171.143 197.560 1.00 48.96 S ATOM 48004 SG CYS B1140 94.930 170.222 193.899 1.00 54.99 S ATOM 48984 SG CYS C 90 90.927 171.892 273.689 1.00 40.19 S ATOM 49019 SG CYS C 94 91.707 170.521 276.233 1.00 32.42 S ATOM 49041 SG CYS C 97 91.477 167.437 274.094 1.00 25.60 S ATOM 56327 SG CYS I 17 149.719 92.855 199.694 1.00 41.99 S ATOM 56351 SG CYS I 20 149.397 96.742 200.040 1.00 41.75 S ATOM 56512 SG CYS I 39 147.083 95.085 198.175 1.00 43.67 S ATOM 56537 SG CYS I 42 151.045 95.158 197.103 1.00 45.80 S ATOM 56889 SG CYS I 86 128.775 78.284 236.997 1.00 47.78 S ATOM 56913 SG CYS I 89 130.941 78.207 240.195 1.00 52.74 S ATOM 57117 SG CYS I 114 129.750 81.344 239.406 1.00 45.61 S ATOM 57152 SG CYS I 119 132.202 79.709 237.037 1.00 43.36 S ATOM 57263 SG CYS J 7 98.437 137.126 271.122 1.00 19.40 S ATOM 57287 SG CYS J 10 95.443 137.317 273.483 1.00 15.55 S ATOM 57551 SG CYS J 44 96.028 134.215 271.675 1.00 22.90 S ATOM 57557 SG CYS J 45 97.809 135.484 274.797 1.00 17.17 S ATOM 58677 SG CYS L 19 133.352 161.050 259.702 1.00 10.00 S ATOM 58696 SG CYS L 22 134.482 161.670 262.786 1.00 14.22 S ATOM 58813 SG CYS L 36 135.267 163.868 260.069 1.00 22.68 S ATOM 59168 SG CYS M 34 94.150 183.350 231.317 1.00 36.93 S ATOM 76483 SG CYS W 129 108.830 194.053 204.294 1.00 55.95 S ATOM 76503 SG CYS W 132 109.487 190.349 203.760 1.00 57.45 S ATOM 76675 SG CYS W 154 105.883 191.641 204.618 1.00 54.08 S ATOM 76699 SG CYS W 157 108.781 191.532 207.075 1.00 59.49 S Time building chain proxies: 32.77, per 1000 atoms: 0.39 Number of scatterers: 84783 At special positions: 0 Unit cell: (227.85, 233.1, 308.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 17 29.99 Fe 4 26.01 S 438 16.00 P 410 15.00 Mg 1 11.99 O 16526 8.00 N 14973 7.00 C 52414 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 - 3.50 Amino acid : False - 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: 29.14 Conformation dependent library (CDL) restraints added in 10.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 11000 " pdb="FE2 SF4 11000 " - pdb=" SG CYS 1 116 " pdb="FE4 SF4 11000 " - pdb=" SG CYS 1 155 " pdb="FE1 SF4 11000 " - pdb=" SG CYS 1 190 " pdb="FE3 SF4 11000 " - pdb=" SG CYS 1 134 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 345 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 368 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 348 " pdb=" ZN 4 402 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 382 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 360 " pdb=" ZN 4 403 " pdb="ZN ZN 4 403 " - pdb=" SG CYS 4 294 " pdb="ZN ZN 4 403 " - pdb=" SG CYS 4 291 " pdb="ZN ZN 4 403 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 403 " - pdb=" SG CYS 4 308 " pdb=" ZN 5 401 " pdb="ZN ZN 5 401 " - pdb=" SG CYS 5 268 " pdb="ZN ZN 5 401 " - pdb=" SG CYS 5 282 " pdb="ZN ZN 5 401 " - pdb=" SG CYS 5 271 " pdb=" ZN 5 402 " pdb="ZN ZN 5 402 " - pdb=" SG CYS 5 276 " pdb="ZN ZN 5 402 " - pdb=" ND1 HIS 5 258 " pdb=" ZN 7 400 " pdb="ZN ZN 7 400 " - pdb=" SG CYS 7 6 " pdb="ZN ZN 7 400 " - pdb=" SG CYS 7 34 " pdb=" ZN 7 401 " pdb="ZN ZN 7 401 " - pdb=" SG CYS 7 26 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" ND1 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 157 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 132 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " Number of angles added : 45 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 389 helices and 74 sheets defined 43.4% alpha, 11.4% beta 131 base pairs and 365 stacking pairs defined. Time for finding SS restraints: 29.67 Creating SS restraints... Processing helix chain '0' and resid 93 through 103 Processing helix chain '0' and resid 120 through 129 Processing helix chain '0' and resid 133 through 143 Processing helix chain '0' and resid 150 through 161 Processing helix chain '0' and resid 183 through 188 removed outlier: 3.532A pdb=" N HIS 0 187 " --> pdb=" O ASP 0 183 " (cutoff:3.500A) Processing helix chain '0' and resid 192 through 197 Processing helix chain '0' and resid 274 through 286 removed outlier: 4.530A pdb=" N GLU 0 278 " --> pdb=" O GLU 0 275 " (cutoff:3.500A) Processing helix chain '0' and resid 318 through 327 Processing helix chain '0' and resid 342 through 344 No H-bonds generated for 'chain '0' and resid 342 through 344' Processing helix chain '0' and resid 346 through 357 Processing helix chain '0' and resid 368 through 381 Processing helix chain '0' and resid 386 through 388 No H-bonds generated for 'chain '0' and resid 386 through 388' Processing helix chain '0' and resid 400 through 402 No H-bonds generated for 'chain '0' and resid 400 through 402' Processing helix chain '0' and resid 410 through 413 No H-bonds generated for 'chain '0' and resid 410 through 413' Processing helix chain '0' and resid 421 through 432 removed outlier: 3.639A pdb=" N VAL 0 426 " --> pdb=" O GLU 0 422 " (cutoff:3.500A) Processing helix chain '0' and resid 443 through 445 No H-bonds generated for 'chain '0' and resid 443 through 445' Processing helix chain '0' and resid 451 through 457 Processing helix chain '0' and resid 477 through 483 removed outlier: 3.630A pdb=" N LEU 0 483 " --> pdb=" O LEU 0 480 " (cutoff:3.500A) Processing helix chain '0' and resid 493 through 498 Processing helix chain '0' and resid 516 through 524 Processing helix chain '0' and resid 528 through 535 removed outlier: 3.781A pdb=" N TYR 0 534 " --> pdb=" O ILE 0 531 " (cutoff:3.500A) Processing helix chain '0' and resid 538 through 553 Processing helix chain '0' and resid 565 through 574 Processing helix chain '0' and resid 586 through 598 Processing helix chain '0' and resid 609 through 613 Processing helix chain '0' and resid 633 through 642 removed outlier: 3.720A pdb=" N ARG 0 642 " --> pdb=" O GLN 0 638 " (cutoff:3.500A) Processing helix chain '0' and resid 652 through 654 No H-bonds generated for 'chain '0' and resid 652 through 654' Processing helix chain '0' and resid 668 through 683 removed outlier: 3.594A pdb=" N ARG 0 678 " --> pdb=" O THR 0 674 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE 0 679 " --> pdb=" O LYS 0 675 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU 0 680 " --> pdb=" O ARG 0 676 " (cutoff:3.500A) Processing helix chain '0' and resid 706 through 719 Processing helix chain '1' and resid 19 through 34 removed outlier: 3.513A pdb=" N SER 1 23 " --> pdb=" O PRO 1 19 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG 1 30 " --> pdb=" O ARG 1 26 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR 1 31 " --> pdb=" O GLU 1 27 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU 1 32 " --> pdb=" O LEU 1 28 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 62 Processing helix chain '1' and resid 77 through 98 removed outlier: 3.541A pdb=" N LYS 1 82 " --> pdb=" O PRO 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 119 through 122 No H-bonds generated for 'chain '1' and resid 119 through 122' Processing helix chain '1' and resid 127 through 138 Processing helix chain '1' and resid 140 through 147 Processing helix chain '1' and resid 156 through 163 Processing helix chain '1' and resid 177 through 187 Processing helix chain '1' and resid 191 through 201 removed outlier: 4.281A pdb=" N LEU 1 200 " --> pdb=" O ARG 1 196 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS 1 201 " --> pdb=" O TYR 1 197 " (cutoff:3.500A) Processing helix chain '1' and resid 209 through 213 removed outlier: 3.650A pdb=" N LEU 1 213 " --> pdb=" O HIS 1 210 " (cutoff:3.500A) Processing helix chain '1' and resid 215 through 221 removed outlier: 3.828A pdb=" N LEU 1 220 " --> pdb=" O LYS 1 216 " (cutoff:3.500A) Processing helix chain '1' and resid 224 through 228 removed outlier: 4.520A pdb=" N LYS 1 228 " --> pdb=" O LEU 1 225 " (cutoff:3.500A) Processing helix chain '1' and resid 239 through 247 Processing helix chain '1' and resid 253 through 276 Processing helix chain '1' and resid 281 through 290 removed outlier: 3.544A pdb=" N ARG 1 286 " --> pdb=" O ASP 1 283 " (cutoff:3.500A) Processing helix chain '1' and resid 326 through 345 Processing helix chain '1' and resid 354 through 364 removed outlier: 4.319A pdb=" N LEU 1 358 " --> pdb=" O PRO 1 354 " (cutoff:3.500A) Processing helix chain '1' and resid 369 through 385 removed outlier: 3.937A pdb=" N PHE 1 374 " --> pdb=" O LYS 1 370 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS 1 375 " --> pdb=" O PRO 1 371 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA 1 376 " --> pdb=" O LEU 1 372 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU 1 377 " --> pdb=" O ARG 1 373 " (cutoff:3.500A) Processing helix chain '1' and resid 391 through 409 Proline residue: 1 396 - end of helix Processing helix chain '1' and resid 441 through 450 Proline residue: 1 446 - end of helix Processing helix chain '1' and resid 464 through 470 Proline residue: 1 468 - end of helix Processing helix chain '1' and resid 514 through 530 Processing helix chain '1' and resid 542 through 554 Processing helix chain '1' and resid 557 through 564 Processing helix chain '1' and resid 574 through 589 Processing helix chain '1' and resid 603 through 607 Processing helix chain '1' and resid 631 through 642 Processing helix chain '1' and resid 648 through 667 removed outlier: 3.588A pdb=" N ARG 1 666 " --> pdb=" O GLN 1 662 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA 1 667 " --> pdb=" O CYS 1 663 " (cutoff:3.500A) Processing helix chain '1' and resid 682 through 685 Processing helix chain '1' and resid 687 through 692 Processing helix chain '1' and resid 695 through 700 Processing helix chain '1' and resid 703 through 706 No H-bonds generated for 'chain '1' and resid 703 through 706' Processing helix chain '1' and resid 710 through 725 Processing helix chain '2' and resid 109 through 120 removed outlier: 4.373A pdb=" N LYS 2 114 " --> pdb=" O GLU 2 110 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN 2 115 " --> pdb=" O LEU 2 111 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN 2 119 " --> pdb=" O ASN 2 115 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 133 removed outlier: 3.862A pdb=" N VAL 2 132 " --> pdb=" O TYR 2 128 " (cutoff:3.500A) Processing helix chain '2' and resid 140 through 145 removed outlier: 3.709A pdb=" N TRP 2 143 " --> pdb=" O GLU 2 140 " (cutoff:3.500A) Processing helix chain '2' and resid 191 through 199 Processing helix chain '2' and resid 201 through 209 Processing helix chain '2' and resid 217 through 225 Processing helix chain '2' and resid 298 through 317 removed outlier: 3.811A pdb=" N ILE 2 303 " --> pdb=" O SER 2 299 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE 2 304 " --> pdb=" O ASN 2 300 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 383 Processing helix chain '2' and resid 397 through 412 removed outlier: 3.910A pdb=" N ILE 2 401 " --> pdb=" O SER 2 397 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU 2 412 " --> pdb=" O ARG 2 408 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 421 No H-bonds generated for 'chain '2' and resid 418 through 421' Processing helix chain '2' and resid 424 through 434 Processing helix chain '2' and resid 456 through 477 removed outlier: 3.755A pdb=" N HIS 2 474 " --> pdb=" O GLU 2 470 " (cutoff:3.500A) Processing helix chain '2' and resid 486 through 517 removed outlier: 3.559A pdb=" N LYS 2 492 " --> pdb=" O GLU 2 488 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS 2 504 " --> pdb=" O PHE 2 500 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU 2 505 " --> pdb=" O GLN 2 501 " (cutoff:3.500A) Proline residue: 2 507 - end of helix Processing helix chain '2' and resid 524 through 546 removed outlier: 3.736A pdb=" N LEU 2 529 " --> pdb=" O ILE 2 525 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 24 Processing helix chain '3' and resid 28 through 34 removed outlier: 4.733A pdb=" N ARG 3 33 " --> pdb=" O GLY 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 40 through 47 Processing helix chain '3' and resid 52 through 61 removed outlier: 4.894A pdb=" N PHE 3 61 " --> pdb=" O MET 3 57 " (cutoff:3.500A) Processing helix chain '3' and resid 68 through 73 Processing helix chain '3' and resid 80 through 92 Processing helix chain '3' and resid 112 through 123 removed outlier: 3.810A pdb=" N LEU 3 123 " --> pdb=" O ARG 3 119 " (cutoff:3.500A) Processing helix chain '3' and resid 145 through 163 Processing helix chain '3' and resid 173 through 181 Processing helix chain '3' and resid 198 through 204 Processing helix chain '3' and resid 208 through 225 Processing helix chain '3' and resid 230 through 240 Processing helix chain '3' and resid 256 through 267 Processing helix chain '3' and resid 285 through 292 removed outlier: 5.864A pdb=" N SER 3 291 " --> pdb=" O ALA 3 287 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER 3 292 " --> pdb=" O ILE 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 322 through 330 Processing helix chain '3' and resid 348 through 357 Processing helix chain '3' and resid 361 through 371 Processing helix chain '3' and resid 385 through 398 Processing helix chain '3' and resid 415 through 428 Processing helix chain '3' and resid 445 through 461 removed outlier: 3.979A pdb=" N ASP 3 450 " --> pdb=" O ALA 3 446 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 12 No H-bonds generated for 'chain '4' and resid 10 through 12' Processing helix chain '4' and resid 18 through 21 Processing helix chain '4' and resid 69 through 72 Processing helix chain '4' and resid 80 through 98 removed outlier: 3.584A pdb=" N TYR 4 90 " --> pdb=" O LYS 4 86 " (cutoff:3.500A) Processing helix chain '4' and resid 124 through 136 removed outlier: 4.722A pdb=" N ASP 4 136 " --> pdb=" O LYS 4 132 " (cutoff:3.500A) Processing helix chain '4' and resid 145 through 158 removed outlier: 5.024A pdb=" N HIS 4 158 " --> pdb=" O GLN 4 154 " (cutoff:3.500A) Processing helix chain '4' and resid 182 through 191 Processing helix chain '4' and resid 206 through 215 Processing helix chain '4' and resid 225 through 236 Processing helix chain '4' and resid 315 through 325 removed outlier: 3.947A pdb=" N SER 4 321 " --> pdb=" O HIS 4 317 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR 4 322 " --> pdb=" O LEU 4 318 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS 4 323 " --> pdb=" O ALA 4 319 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N HIS 4 324 " --> pdb=" O ARG 4 320 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU 4 325 " --> pdb=" O SER 4 321 " (cutoff:3.500A) Processing helix chain '4' and resid 369 through 377 Processing helix chain '5' and resid 19 through 27 Processing helix chain '5' and resid 34 through 51 Processing helix chain '5' and resid 102 through 120 Processing helix chain '5' and resid 134 through 150 Processing helix chain '5' and resid 171 through 186 removed outlier: 4.099A pdb=" N MET 5 175 " --> pdb=" O LEU 5 172 " (cutoff:3.500A) Processing helix chain '5' and resid 201 through 210 removed outlier: 3.690A pdb=" N ASP 5 208 " --> pdb=" O GLN 5 204 " (cutoff:3.500A) Processing helix chain '5' and resid 220 through 229 removed outlier: 4.963A pdb=" N LEU 5 224 " --> pdb=" O PRO 5 221 " (cutoff:3.500A) Processing helix chain '5' and resid 235 through 239 Processing helix chain '6' and resid 14 through 25 removed outlier: 3.553A pdb=" N ASP 6 24 " --> pdb=" O LEU 6 20 " (cutoff:3.500A) Processing helix chain '6' and resid 47 through 64 removed outlier: 3.589A pdb=" N VAL 6 50 " --> pdb=" O ALA 6 47 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN 6 51 " --> pdb=" O GLU 6 48 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 15 No H-bonds generated for 'chain '7' and resid 12 through 15' Processing helix chain '7' and resid 32 through 40 removed outlier: 4.484A pdb=" N LEU 7 37 " --> pdb=" O SER 7 33 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL 7 40 " --> pdb=" O ASP 7 36 " (cutoff:3.500A) Processing helix chain '7' and resid 66 through 80 removed outlier: 4.262A pdb=" N LYS 7 80 " --> pdb=" O LYS 7 76 " (cutoff:3.500A) Processing helix chain '7' and resid 86 through 88 No H-bonds generated for 'chain '7' and resid 86 through 88' Processing helix chain '7' and resid 92 through 110 removed outlier: 4.058A pdb=" N ASN 7 96 " --> pdb=" O LEU 7 92 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE 7 98 " --> pdb=" O GLU 7 94 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU 7 99 " --> pdb=" O TYR 7 95 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU 7 101 " --> pdb=" O ASP 7 97 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 128 removed outlier: 4.141A pdb=" N LYS 7 127 " --> pdb=" O GLU 7 123 " (cutoff:3.500A) Processing helix chain '7' and resid 132 through 148 removed outlier: 3.627A pdb=" N LEU 7 138 " --> pdb=" O GLN 7 134 " (cutoff:3.500A) Processing helix chain '7' and resid 263 through 266 No H-bonds generated for 'chain '7' and resid 263 through 266' Processing helix chain '7' and resid 268 through 272 Processing helix chain '7' and resid 280 through 284 Processing helix chain '7' and resid 289 through 301 Processing helix chain '8' and resid 46 through 49 No H-bonds generated for 'chain '8' and resid 46 through 49' Processing helix chain '8' and resid 57 through 68 removed outlier: 3.643A pdb=" N GLU 8 68 " --> pdb=" O LYS 8 64 " (cutoff:3.500A) Processing helix chain '8' and resid 99 through 103 Processing helix chain '8' and resid 111 through 131 Processing helix chain '8' and resid 176 through 178 No H-bonds generated for 'chain '8' and resid 176 through 178' Processing helix chain '8' and resid 181 through 184 No H-bonds generated for 'chain '8' and resid 181 through 184' Processing helix chain '8' and resid 192 through 208 removed outlier: 3.566A pdb=" N ALA 8 198 " --> pdb=" O VAL 8 194 " (cutoff:3.500A) Processing helix chain '8' and resid 218 through 229 Processing helix chain '8' and resid 240 through 242 No H-bonds generated for 'chain '8' and resid 240 through 242' Processing helix chain '8' and resid 257 through 260 No H-bonds generated for 'chain '8' and resid 257 through 260' Processing helix chain '8' and resid 266 through 276 Processing helix chain '8' and resid 286 through 291 Processing helix chain '8' and resid 293 through 296 No H-bonds generated for 'chain '8' and resid 293 through 296' Processing helix chain '8' and resid 304 through 306 No H-bonds generated for 'chain '8' and resid 304 through 306' Processing helix chain '9' and resid 3 through 5 No H-bonds generated for 'chain '9' and resid 3 through 5' Processing helix chain '9' and resid 7 through 10 No H-bonds generated for 'chain '9' and resid 7 through 10' Processing helix chain '9' and resid 16 through 36 Processing helix chain '9' and resid 50 through 70 Processing helix chain '9' and resid 77 through 91 Processing helix chain '9' and resid 101 through 115 Processing helix chain '9' and resid 122 through 128 Processing helix chain '9' and resid 133 through 153 removed outlier: 4.301A pdb=" N LEU 9 148 " --> pdb=" O LEU 9 144 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU 9 149 " --> pdb=" O GLU 9 145 " (cutoff:3.500A) Processing helix chain '9' and resid 163 through 177 removed outlier: 4.016A pdb=" N LYS 9 175 " --> pdb=" O LEU 9 171 " (cutoff:3.500A) Processing helix chain '9' and resid 184 through 200 removed outlier: 3.823A pdb=" N LYS 9 189 " --> pdb=" O ILE 9 186 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP 9 192 " --> pdb=" O LYS 9 189 " (cutoff:3.500A) Processing helix chain '9' and resid 203 through 206 No H-bonds generated for 'chain '9' and resid 203 through 206' Processing helix chain '9' and resid 209 through 224 Processing helix chain '9' and resid 229 through 233 Processing helix chain '9' and resid 238 through 261 removed outlier: 4.013A pdb=" N ARG 9 242 " --> pdb=" O LYS 9 239 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR 9 243 " --> pdb=" O GLU 9 240 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU 9 245 " --> pdb=" O ARG 9 242 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER 9 246 " --> pdb=" O THR 9 243 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET 9 255 " --> pdb=" O MET 9 252 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS 9 261 " --> pdb=" O LEU 9 258 " (cutoff:3.500A) Processing helix chain '9' and resid 267 through 281 removed outlier: 3.631A pdb=" N GLN 9 275 " --> pdb=" O ALA 9 271 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS 9 280 " --> pdb=" O LYS 9 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 97 through 109 removed outlier: 5.358A pdb=" N VAL A 101 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 108 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.947A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 275 through 295 Processing helix chain 'A' and resid 300 through 318 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 487 through 492 Proline residue: A 491 - end of helix Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 557 through 565 removed outlier: 3.626A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.552A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 614 Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 662 through 683 removed outlier: 3.778A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 772 Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 833 through 856 removed outlier: 3.605A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.531A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 944 Processing helix chain 'A' and resid 946 through 969 Processing helix chain 'A' and resid 983 through 993 Processing helix chain 'A' and resid 1006 through 1019 Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1051 through 1056 Processing helix chain 'A' and resid 1062 through 1079 removed outlier: 3.516A pdb=" N ALA A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1101 Proline residue: A1098 - end of helix removed outlier: 3.885A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 Processing helix chain 'A' and resid 1146 through 1148 No H-bonds generated for 'chain 'A' and resid 1146 through 1148' Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 3.503A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1181 through 1183 No H-bonds generated for 'chain 'A' and resid 1181 through 1183' Processing helix chain 'A' and resid 1187 through 1197 removed outlier: 4.123A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1228 through 1242 removed outlier: 7.276A pdb=" N ASP A1241 " --> pdb=" O ALA A1237 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASP A1242 " --> pdb=" O GLY A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1283 through 1292 removed outlier: 3.537A pdb=" N SER A1290 " --> pdb=" O CYS A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1371 through 1388 removed outlier: 3.533A pdb=" N GLU A1379 " --> pdb=" O ARG A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1407 Processing helix chain 'A' and resid 1416 through 1421 removed outlier: 5.017A pdb=" N ARG A1421 " --> pdb=" O HIS A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 removed outlier: 3.862A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.672A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1459 Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'A' and resid 1479 through 1481 No H-bonds generated for 'chain 'A' and resid 1479 through 1481' Processing helix chain 'B' and resid 19 through 36 removed outlier: 4.353A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 281 through 288 removed outlier: 3.991A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 324 Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 358 through 377 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 424 Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 492 through 495 No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 539 through 547 removed outlier: 3.725A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 555 No H-bonds generated for 'chain 'B' and resid 553 through 555' Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.919A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 672' Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 731 removed outlier: 4.031A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 765 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 975 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 978 through 993 Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.608A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1058 No H-bonds generated for 'chain 'B' and resid 1055 through 1058' Processing helix chain 'B' and resid 1088 through 1097 Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.531A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 78 through 81 No H-bonds generated for 'chain 'C' and resid 78 through 81' Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 270 Processing helix chain 'D' and resid 24 through 27 No H-bonds generated for 'chain 'D' and resid 24 through 27' Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 70 Processing helix chain 'D' and resid 77 through 89 removed outlier: 3.695A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'E' and resid 3 through 23 removed outlier: 4.113A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 42 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 121 removed outlier: 3.584A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 162 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'H' and resid 129 through 132 No H-bonds generated for 'chain 'H' and resid 129 through 132' Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.719A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.853A pdb=" N LEU J 60 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 Processing helix chain 'K' and resid 40 through 51 removed outlier: 3.755A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 114 Processing helix chain 'M' and resid 48 through 51 No H-bonds generated for 'chain 'M' and resid 48 through 51' Processing helix chain 'M' and resid 109 through 127 Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 156 through 170 Processing helix chain 'M' and resid 177 through 183 Processing helix chain 'M' and resid 188 through 202 Processing helix chain 'M' and resid 211 through 221 removed outlier: 3.584A pdb=" N PHE M 214 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET M 215 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N SER M 216 " --> pdb=" O ASP M 213 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS M 219 " --> pdb=" O SER M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 241 Processing helix chain 'M' and resid 250 through 264 Processing helix chain 'M' and resid 271 through 278 Processing helix chain 'M' and resid 282 through 299 Proline residue: M 294 - end of helix Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 310 through 312 No H-bonds generated for 'chain 'M' and resid 310 through 312' Processing helix chain 'O' and resid 180 through 186 Processing helix chain 'O' and resid 227 through 243 Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'O' and resid 318 through 334 Proline residue: O 330 - end of helix Processing helix chain 'Q' and resid 6 through 8 No H-bonds generated for 'chain 'Q' and resid 6 through 8' Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 157 through 168 removed outlier: 4.364A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG Q 167 " --> pdb=" O GLU Q 163 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN Q 168 " --> pdb=" O TRP Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 179 removed outlier: 3.713A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 13 Processing helix chain 'R' and resid 25 through 33 Processing helix chain 'R' and resid 60 through 63 No H-bonds generated for 'chain 'R' and resid 60 through 63' Processing helix chain 'R' and resid 122 through 136 removed outlier: 3.685A pdb=" N ARG R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 172 Processing helix chain 'R' and resid 180 through 193 Processing helix chain 'R' and resid 199 through 206 Processing helix chain 'R' and resid 210 through 219 removed outlier: 3.828A pdb=" N GLU R 219 " --> pdb=" O GLU R 215 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 32 removed outlier: 4.409A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 50 Processing helix chain 'U' and resid 325 through 329 removed outlier: 3.909A pdb=" N PHE U 329 " --> pdb=" O GLN U 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 8 No H-bonds generated for 'chain 'V' and resid 6 through 8' Processing helix chain 'V' and resid 10 through 24 removed outlier: 3.962A pdb=" N LEU V 15 " --> pdb=" O LEU V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 50 removed outlier: 3.624A pdb=" N LEU V 34 " --> pdb=" O PRO V 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 25 Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 45 through 52 Processing helix chain 'W' and resid 56 through 68 Processing helix chain 'W' and resid 96 through 123 Processing helix chain 'W' and resid 138 through 144 removed outlier: 4.359A pdb=" N ASN W 142 " --> pdb=" O LEU W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 194 removed outlier: 3.692A pdb=" N ALA W 167 " --> pdb=" O ASP W 164 " (cutoff:3.500A) Proline residue: W 169 - end of helix removed outlier: 3.761A pdb=" N ASP W 172 " --> pdb=" O PRO W 169 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA W 173 " --> pdb=" O LYS W 170 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU W 177 " --> pdb=" O ARG W 174 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA W 178 " --> pdb=" O THR W 175 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG W 179 " --> pdb=" O LEU W 176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN W 183 " --> pdb=" O PHE W 180 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE W 184 " --> pdb=" O ASN W 181 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU W 185 " --> pdb=" O GLU W 182 " (cutoff:3.500A) Proline residue: W 186 - end of helix Processing helix chain 'W' and resid 279 through 282 No H-bonds generated for 'chain 'W' and resid 279 through 282' Processing helix chain 'X' and resid 75 through 91 removed outlier: 3.697A pdb=" N GLN X 90 " --> pdb=" O LYS X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 106 Processing helix chain 'X' and resid 113 through 121 Processing helix chain 'X' and resid 123 through 126 No H-bonds generated for 'chain 'X' and resid 123 through 126' Processing helix chain 'X' and resid 148 through 160 Processing helix chain 'X' and resid 168 through 174 Processing helix chain 'X' and resid 178 through 188 removed outlier: 3.864A pdb=" N LYS X 183 " --> pdb=" O LYS X 180 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP X 187 " --> pdb=" O ALA X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 222 Processing helix chain 'X' and resid 230 through 240 removed outlier: 4.094A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS X 238 " --> pdb=" O GLU X 234 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN X 240 " --> pdb=" O TYR X 236 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 57 Processing helix chain 'a' and resid 65 through 79 removed outlier: 3.789A pdb=" N ASP a 78 " --> pdb=" O GLU a 74 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE a 79 " --> pdb=" O ILE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 114 Processing helix chain 'a' and resid 122 through 132 Processing helix chain 'b' and resid 26 through 29 Processing helix chain 'b' and resid 32 through 41 Processing helix chain 'b' and resid 51 through 76 Processing helix chain 'b' and resid 84 through 93 Processing helix chain 'c' and resid 18 through 21 No H-bonds generated for 'chain 'c' and resid 18 through 21' Processing helix chain 'c' and resid 28 through 37 Processing helix chain 'c' and resid 46 through 73 removed outlier: 3.951A pdb=" N VAL c 50 " --> pdb=" O ALA c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 90 Processing helix chain 'c' and resid 92 through 97 Processing helix chain 'd' and resid 39 through 49 Processing helix chain 'd' and resid 57 through 84 Processing helix chain 'd' and resid 92 through 102 Processing helix chain 'd' and resid 105 through 124 Processing helix chain 'e' and resid 46 through 57 removed outlier: 3.528A pdb=" N ARG e 53 " --> pdb=" O LEU e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 65 through 78 removed outlier: 3.804A pdb=" N ASP e 78 " --> pdb=" O GLU e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 87 through 114 Processing helix chain 'e' and resid 122 through 131 Processing helix chain 'f' and resid 32 through 41 Processing helix chain 'f' and resid 51 through 76 Processing helix chain 'f' and resid 84 through 94 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 28 through 37 Processing helix chain 'g' and resid 46 through 73 removed outlier: 4.008A pdb=" N VAL g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 90 Processing helix chain 'g' and resid 94 through 97 No H-bonds generated for 'chain 'g' and resid 94 through 97' Processing helix chain 'h' and resid 39 through 49 Processing helix chain 'h' and resid 57 through 84 Processing helix chain 'h' and resid 92 through 102 Processing helix chain 'h' and resid 105 through 125 Processing sheet with id= A, first strand: chain '0' and resid 76 through 78 removed outlier: 5.744A pdb=" N LYS 0 117 " --> pdb=" O PRO 0 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '0' and resid 166 through 171 removed outlier: 4.562A pdb=" N TYR 0 175 " --> pdb=" O VAL 0 272 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '0' and resid 389 through 391 removed outlier: 6.690A pdb=" N VAL 0 405 " --> pdb=" O CYS 0 390 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA 0 406 " --> pdb=" O CYS 0 361 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU 0 437 " --> pdb=" O LEU 0 362 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU 0 364 " --> pdb=" O LEU 0 437 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE 0 439 " --> pdb=" O LEU 0 364 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N CYS 0 462 " --> pdb=" O MET 0 438 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU 0 440 " --> pdb=" O CYS 0 462 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU 0 464 " --> pdb=" O LEU 0 440 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY 0 336 " --> pdb=" O GLY 0 465 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR 0 467 " --> pdb=" O GLY 0 336 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE 0 338 " --> pdb=" O THR 0 467 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL 0 339 " --> pdb=" O LEU 0 488 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU 0 490 " --> pdb=" O VAL 0 339 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '0' and resid 688 through 690 removed outlier: 7.354A pdb=" N ALA 0 657 " --> pdb=" O GLN 0 506 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA 0 508 " --> pdb=" O ALA 0 657 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE 0 659 " --> pdb=" O ALA 0 508 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL 0 510 " --> pdb=" O PHE 0 659 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER 0 661 " --> pdb=" O VAL 0 510 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS 0 512 " --> pdb=" O SER 0 661 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL 0 663 " --> pdb=" O CYS 0 512 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 2 through 4 Processing sheet with id= F, first strand: chain '1' and resid 478 through 480 removed outlier: 7.086A pdb=" N VAL 1 39 " --> pdb=" O ALA 1 479 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER 1 458 " --> pdb=" O LEU 1 40 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER 1 74 " --> pdb=" O TYR 1 207 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY 1 173 " --> pdb=" O GLY 1 106 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ALA 1 108 " --> pdb=" O GLY 1 173 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TYR 1 175 " --> pdb=" O ALA 1 108 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 249 through 252 removed outlier: 3.578A pdb=" N VAL 1 249 " --> pdb=" O PHE 1 435 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '1' and resid 490 through 494 removed outlier: 7.214A pdb=" N GLY 1 675 " --> pdb=" O CYS 1 491 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N MET 1 493 " --> pdb=" O GLY 1 675 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N MET 1 677 " --> pdb=" O MET 1 493 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE 1 535 " --> pdb=" O ALA 1 594 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU 1 566 " --> pdb=" O ILE 1 595 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU 1 597 " --> pdb=" O LEU 1 566 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE 1 568 " --> pdb=" O LEU 1 597 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL 1 599 " --> pdb=" O PHE 1 568 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 307 through 309 removed outlier: 6.279A pdb=" N GLN 3 345 " --> pdb=" O MET 3 334 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N MET 3 334 " --> pdb=" O GLN 3 345 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 407 through 409 removed outlier: 3.534A pdb=" N TYR 3 409 " --> pdb=" O MET 3 441 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET 3 441 " --> pdb=" O TYR 3 409 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '4' and resid 113 through 118 removed outlier: 6.523A pdb=" N ILE 4 106 " --> pdb=" O LEU 4 117 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER 4 164 " --> pdb=" O HIS 4 60 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR 4 62 " --> pdb=" O SER 4 164 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU 4 166 " --> pdb=" O TYR 4 62 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL 4 64 " --> pdb=" O GLU 4 166 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU 4 168 " --> pdb=" O VAL 4 64 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ASP 4 66 " --> pdb=" O LEU 4 168 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE 4 170 " --> pdb=" O ASP 4 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG 4 195 " --> pdb=" O VAL 4 167 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE 4 169 " --> pdb=" O ARG 4 195 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER 4 197 " --> pdb=" O ILE 4 169 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE 4 171 " --> pdb=" O SER 4 197 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE 4 199 " --> pdb=" O PHE 4 171 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 357 through 359 Processing sheet with id= M, first strand: chain '5' and resid 67 through 69 removed outlier: 6.356A pdb=" N LYS 5 158 " --> pdb=" O LEU 5 10 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL 5 12 " --> pdb=" O LYS 5 158 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG 5 160 " --> pdb=" O VAL 5 12 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL 5 14 " --> pdb=" O ARG 5 160 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU 5 162 " --> pdb=" O VAL 5 14 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU 5 190 " --> pdb=" O ILE 5 161 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL 5 163 " --> pdb=" O LEU 5 190 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP 5 192 " --> pdb=" O VAL 5 163 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '6' and resid 8 through 11 removed outlier: 3.769A pdb=" N PHE 6 44 " --> pdb=" O GLN 6 36 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN 6 36 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '7' and resid 21 through 23 removed outlier: 3.535A pdb=" N LEU 7 21 " --> pdb=" O GLN 7 61 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '8' and resid 77 through 83 removed outlier: 6.619A pdb=" N VAL 8 90 " --> pdb=" O LEU 8 78 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA 8 80 " --> pdb=" O SER 8 88 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER 8 88 " --> pdb=" O ALA 8 80 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLY 8 82 " --> pdb=" O ASN 8 86 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN 8 86 " --> pdb=" O GLY 8 82 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ARG 8 30 " --> pdb=" O LYS 8 14 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LYS 8 14 " --> pdb=" O ARG 8 30 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 86 through 89 Processing sheet with id= R, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.908A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.830A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 362 through 366 removed outlier: 3.684A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 367 through 369 removed outlier: 5.916A pdb=" N PHE A 482 " --> pdb=" O THR A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'A' and resid 389 through 393 Processing sheet with id= W, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= X, first strand: chain 'A' and resid 554 through 556 Processing sheet with id= Y, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.548A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 902 through 905 Processing sheet with id= AA, first strand: chain 'A' and resid 1139 through 1142 removed outlier: 3.775A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.142A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id= AD, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.205A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= AF, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= AG, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= AH, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.852A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 484 through 486 Processing sheet with id= AJ, first strand: chain 'B' and resid 530 through 532 Processing sheet with id= AK, first strand: chain 'B' and resid 602 through 606 removed outlier: 3.507A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.816A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 1042 through 1048 removed outlier: 4.356A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 965 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET B 796 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN B 948 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 827 through 829 Processing sheet with id= AO, first strand: chain 'B' and resid 934 through 936 Processing sheet with id= AP, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id= AQ, first strand: chain 'B' and resid 121 through 126 removed outlier: 6.283A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.460A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 98 through 106 removed outlier: 5.952A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'C' and resid 113 through 116 Processing sheet with id= AU, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.841A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'E' and resid 147 through 150 Processing sheet with id= AW, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AX, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.803A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR G 37 " --> pdb=" O VAL G 45 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'G' and resid 83 through 87 removed outlier: 3.598A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'G' and resid 117 through 119 Processing sheet with id= BA, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.429A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'H' and resid 26 through 31 removed outlier: 5.195A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'I' and resid 24 through 28 removed outlier: 4.039A pdb=" N TYR I 44 " --> pdb=" O CYS I 39 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= BE, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= BF, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= BG, first strand: chain 'M' and resid 24 through 26 Processing sheet with id= BH, first strand: chain 'O' and resid 170 through 173 removed outlier: 3.957A pdb=" N LYS O 218 " --> pdb=" O PHE O 214 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'O' and resid 291 through 294 removed outlier: 3.523A pdb=" N GLY O 314 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N MET O 258 " --> pdb=" O GLY O 314 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER O 261 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU O 165 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Q' and resid 15 through 17 removed outlier: 4.189A pdb=" N GLU Q 136 " --> pdb=" O THR Q 128 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR Q 128 " --> pdb=" O GLU Q 136 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'Q' and resid 27 through 31 removed outlier: 6.658A pdb=" N ASN Q 142 " --> pdb=" O ILE Q 28 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ALA Q 30 " --> pdb=" O ASN Q 142 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR Q 144 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'R' and resid 41 through 47 removed outlier: 9.755A pdb=" N THR R 52 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU R 85 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL R 54 " --> pdb=" O PHE R 83 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG R 113 " --> pdb=" O GLN R 86 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU R 20 " --> pdb=" O VAL R 111 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG R 113 " --> pdb=" O LEU R 20 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LYS R 22 " --> pdb=" O ARG R 113 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU R 115 " --> pdb=" O LYS R 22 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'R' and resid 222 through 224 Processing sheet with id= BN, first strand: chain 'R' and resid 94 through 99 removed outlier: 6.509A pdb=" N THR R 97 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU R 106 " --> pdb=" O THR R 97 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER R 99 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU R 104 " --> pdb=" O SER R 99 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'U' and resid 341 through 345 Processing sheet with id= BP, first strand: chain 'U' and resid 363 through 367 removed outlier: 6.618A pdb=" N GLN U 338 " --> pdb=" O LYS U 354 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY U 356 " --> pdb=" O VAL U 336 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL U 336 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N MET U 358 " --> pdb=" O VAL U 334 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL U 334 " --> pdb=" O MET U 358 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'V' and resid 56 through 59 Processing sheet with id= BR, first strand: chain 'V' and resid 92 through 97 removed outlier: 6.364A pdb=" N ASN V 77 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU V 62 " --> pdb=" O ASN V 77 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'W' and resid 42 through 44 Processing sheet with id= BT, first strand: chain 'W' and resid 127 through 129 Processing sheet with id= BU, first strand: chain 'X' and resid 131 through 133 Processing sheet with id= BV, first strand: chain 'X' and resid 189 through 193 3056 hydrogen bonds defined for protein. 8487 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 325 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 365 stacking parallelities Total time for adding SS restraints: 42.37 Time building geometry restraints manager: 31.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 35095 1.40 - 1.62: 51462 1.62 - 1.84: 675 1.84 - 2.06: 1 2.06 - 2.28: 12 Bond restraints: 87245 Sorted by residual: bond pdb=" C ARG J 6 " pdb=" O ARG J 6 " ideal model delta sigma weight residual 1.234 1.185 0.050 1.22e-02 6.72e+03 1.67e+01 bond pdb=" N ARG h 34 " pdb=" CA ARG h 34 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.32e-02 5.74e+03 6.48e+00 bond pdb=" N SER d 33 " pdb=" CA SER d 33 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.31e-02 5.83e+03 6.45e+00 bond pdb=" N ARG c 21 " pdb=" CA ARG c 21 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.18e+00 bond pdb=" N CYS M 37 " pdb=" CA CYS M 37 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.09e+00 ... (remaining 87240 not shown) Histogram of bond angle deviations from ideal: 73.41 - 85.58: 12 85.58 - 97.75: 2 97.75 - 109.92: 17278 109.92 - 122.08: 85993 122.08 - 134.25: 16347 Bond angle restraints: 119632 Sorted by residual: angle pdb=" O3' DG N 10 " pdb=" C3' DG N 10 " pdb=" C2' DG N 10 " ideal model delta sigma weight residual 111.50 103.74 7.76 1.50e+00 4.44e-01 2.68e+01 angle pdb=" C UNK Y 6 " pdb=" N UNK Y 7 " pdb=" CA UNK Y 7 " ideal model delta sigma weight residual 121.70 130.23 -8.53 1.80e+00 3.09e-01 2.25e+01 angle pdb=" N LYS A 910 " pdb=" CA LYS A 910 " pdb=" C LYS A 910 " ideal model delta sigma weight residual 109.81 119.90 -10.09 2.21e+00 2.05e-01 2.08e+01 angle pdb=" C4' DG N 11 " pdb=" O4' DG N 11 " pdb=" C1' DG N 11 " ideal model delta sigma weight residual 109.70 102.89 6.81 1.50e+00 4.44e-01 2.06e+01 angle pdb=" N ARG A 512 " pdb=" CA ARG A 512 " pdb=" C ARG A 512 " ideal model delta sigma weight residual 110.97 106.12 4.85 1.09e+00 8.42e-01 1.98e+01 ... (remaining 119627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 49907 35.92 - 71.84: 2077 71.84 - 107.76: 119 107.76 - 143.68: 1 143.68 - 179.59: 10 Dihedral angle restraints: 52114 sinusoidal: 24257 harmonic: 27857 Sorted by residual: dihedral pdb=" C4' DG N 56 " pdb=" C3' DG N 56 " pdb=" O3' DG N 56 " pdb=" P DA N 57 " ideal model delta sinusoidal sigma weight residual -140.00 39.59 -179.59 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT T -57 " pdb=" C3' DT T -57 " pdb=" O3' DT T -57 " pdb=" P DC T -56 " ideal model delta sinusoidal sigma weight residual -140.00 37.23 -177.23 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC T -12 " pdb=" C3' DC T -12 " pdb=" O3' DC T -12 " pdb=" P DC T -11 " ideal model delta sinusoidal sigma weight residual -140.00 37.09 -177.09 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 52111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 10825 0.067 - 0.134: 2314 0.134 - 0.201: 238 0.201 - 0.268: 28 0.268 - 0.335: 8 Chirality restraints: 13413 Sorted by residual: chirality pdb=" C3' DT T -55 " pdb=" C4' DT T -55 " pdb=" O3' DT T -55 " pdb=" C2' DT T -55 " both_signs ideal model delta sigma weight residual False -2.66 -2.33 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C3' DA T -30 " pdb=" C4' DA T -30 " pdb=" O3' DA T -30 " pdb=" C2' DA T -30 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA GLU C 62 " pdb=" N GLU C 62 " pdb=" C GLU C 62 " pdb=" CB GLU C 62 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 13410 not shown) Planarity restraints: 13950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1482 " -0.004 2.00e-02 2.50e+03 4.14e-02 3.42e+01 pdb=" CG TYR A1482 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR A1482 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR A1482 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A1482 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A1482 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A1482 " 0.059 2.00e-02 2.50e+03 pdb=" OH TYR A1482 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 5 226 " 0.001 2.00e-02 2.50e+03 3.00e-02 1.79e+01 pdb=" CG TYR 5 226 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR 5 226 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR 5 226 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR 5 226 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR 5 226 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR 5 226 " 0.042 2.00e-02 2.50e+03 pdb=" OH TYR 5 226 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 753 " 0.005 2.00e-02 2.50e+03 2.85e-02 1.62e+01 pdb=" CG TYR B 753 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR B 753 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR B 753 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 753 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR B 753 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 753 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR B 753 " 0.045 2.00e-02 2.50e+03 ... (remaining 13947 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 112 2.36 - 3.00: 46108 3.00 - 3.63: 136145 3.63 - 4.27: 209023 4.27 - 4.90: 339950 Nonbonded interactions: 731338 Sorted by model distance: nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 1.730 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.741 2.170 nonbonded pdb=" O GLU C 92 " pdb="ZN ZN C 301 " model vdw 1.988 2.230 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2003 " model vdw 2.026 2.170 nonbonded pdb=" O CYS 7 26 " pdb="ZN ZN 7 401 " model vdw 2.094 2.230 ... (remaining 731333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'a' selection = (chain 'e' and resid 39 through 135) } ncs_group { reference = (chain 'b' and resid 24 through 103) selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 14 through 119) selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 32 through 126) selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 15.910 Check model and map are aligned: 0.940 Set scattering table: 0.590 Process input model: 224.040 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 250.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 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 : 0.006 0.077 87245 Z= 0.378 Angle : 0.897 12.325 119632 Z= 0.529 Chirality : 0.054 0.335 13413 Planarity : 0.010 0.112 13950 Dihedral : 17.059 179.595 34060 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.08), residues: 9382 helix: -0.39 (0.07), residues: 4165 sheet: -0.08 (0.14), residues: 1193 loop : -0.49 (0.10), residues: 4024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP 0 77 HIS 0.014 0.002 HIS 5 258 PHE 0.049 0.003 PHE B 278 TYR 0.061 0.007 TYR A1482 ARG 0.028 0.004 ARG A1258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 696 time to evaluate : 7.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 MET cc_start: -0.2379 (pmm) cc_final: -0.3463 (ptt) REVERT: 2 411 MET cc_start: -0.1993 (ttt) cc_final: -0.4278 (mtt) REVERT: 3 228 MET cc_start: -0.0364 (mmp) cc_final: -0.0781 (ttp) REVERT: 4 273 MET cc_start: -0.1774 (mmp) cc_final: -0.2027 (mmt) REVERT: A 467 MET cc_start: 0.7454 (mpp) cc_final: 0.6968 (mmt) REVERT: A 514 GLU cc_start: 0.8350 (tt0) cc_final: 0.8064 (tt0) REVERT: A 631 GLU cc_start: 0.7755 (tt0) cc_final: 0.7467 (tt0) REVERT: A 687 ILE cc_start: 0.9135 (tp) cc_final: 0.8916 (tt) REVERT: A 865 ILE cc_start: 0.8966 (tp) cc_final: 0.8645 (mt) REVERT: A 1094 SER cc_start: 0.9419 (m) cc_final: 0.9137 (p) REVERT: A 1288 ILE cc_start: 0.8413 (mt) cc_final: 0.7782 (mm) REVERT: B 121 SER cc_start: 0.9082 (m) cc_final: 0.8750 (p) REVERT: B 304 SER cc_start: 0.8654 (m) cc_final: 0.7776 (t) REVERT: B 508 MET cc_start: 0.9031 (mmt) cc_final: 0.8749 (mmm) REVERT: B 1165 MET cc_start: 0.7363 (mtp) cc_final: 0.6655 (mtp) REVERT: G 3 TYR cc_start: 0.4848 (m-80) cc_final: 0.4494 (m-10) REVERT: M 292 ILE cc_start: 0.8262 (pt) cc_final: 0.8033 (pt) REVERT: O 286 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7118 (mt-10) REVERT: V 1 MET cc_start: 0.4391 (ptm) cc_final: 0.2894 (tpt) outliers start: 5 outliers final: 1 residues processed: 701 average time/residue: 0.8337 time to fit residues: 991.2333 Evaluate side-chains 411 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 410 time to evaluate : 7.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 820 optimal weight: 20.0000 chunk 736 optimal weight: 0.8980 chunk 408 optimal weight: 4.9990 chunk 251 optimal weight: 40.0000 chunk 496 optimal weight: 20.0000 chunk 393 optimal weight: 0.8980 chunk 761 optimal weight: 90.0000 chunk 294 optimal weight: 10.0000 chunk 463 optimal weight: 20.0000 chunk 567 optimal weight: 0.9980 chunk 882 optimal weight: 4.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 181 HIS 0 506 GLN 1 201 HIS ** 1 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 258 HIS 7 24 ASN 7 126 GLN 8 86 ASN 9 100 HIS A 313 HIS A 372 ASN A 459 ASN A1005 HIS A1093 GLN A1194 ASN A1291 ASN B 500 GLN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 930 GLN B 941 GLN B1145 GLN C 66 HIS I 100 HIS K 89 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN V 39 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5513 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 87245 Z= 0.284 Angle : 0.641 15.714 119632 Z= 0.345 Chirality : 0.043 0.232 13413 Planarity : 0.004 0.062 13950 Dihedral : 19.719 178.991 14911 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.69 % Allowed : 7.04 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.08), residues: 9382 helix: 0.86 (0.08), residues: 4178 sheet: -0.03 (0.14), residues: 1209 loop : -0.07 (0.10), residues: 3995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 0 77 HIS 0.011 0.001 HIS 3 161 PHE 0.029 0.002 PHE 6 19 TYR 0.023 0.002 TYR 5 101 ARG 0.012 0.000 ARG 9 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 453 time to evaluate : 7.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 MET cc_start: -0.2067 (pmm) cc_final: -0.3070 (ptt) REVERT: 0 412 MET cc_start: -0.0022 (ttt) cc_final: -0.0564 (mtt) REVERT: 2 117 MET cc_start: -0.3338 (ptt) cc_final: -0.4319 (ptt) REVERT: 2 411 MET cc_start: -0.2002 (ttt) cc_final: -0.4062 (mtt) REVERT: 3 216 MET cc_start: -0.1664 (mtp) cc_final: -0.1960 (ptp) REVERT: 3 228 MET cc_start: -0.0469 (mmp) cc_final: -0.1003 (ttt) REVERT: 3 341 MET cc_start: 0.1679 (tmm) cc_final: 0.1369 (tmm) REVERT: 4 273 MET cc_start: -0.1768 (mmp) cc_final: -0.2084 (mmm) REVERT: 6 16 MET cc_start: 0.1802 (mtp) cc_final: 0.1570 (mtm) REVERT: A 329 MET cc_start: 0.6454 (mmp) cc_final: 0.5226 (ttm) REVERT: A 467 MET cc_start: 0.7259 (mpp) cc_final: 0.7007 (mmt) REVERT: A 469 MET cc_start: 0.8296 (mtp) cc_final: 0.7280 (ttt) REVERT: A 687 ILE cc_start: 0.9167 (tp) cc_final: 0.8918 (tt) REVERT: A 1094 SER cc_start: 0.9484 (m) cc_final: 0.9100 (p) REVERT: A 1412 MET cc_start: 0.7680 (mmm) cc_final: 0.7377 (mmm) REVERT: B 121 SER cc_start: 0.9128 (m) cc_final: 0.8789 (p) REVERT: B 298 MET cc_start: 0.8181 (mmm) cc_final: 0.7862 (mpp) REVERT: B 304 SER cc_start: 0.8724 (m) cc_final: 0.7959 (t) REVERT: B 733 MET cc_start: 0.8145 (mtt) cc_final: 0.7869 (mtm) REVERT: B 1046 THR cc_start: 0.8766 (m) cc_final: 0.8460 (p) REVERT: B 1161 GLU cc_start: 0.7715 (tm-30) cc_final: 0.6353 (tm-30) REVERT: C 41 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7666 (mt-10) REVERT: O 219 MET cc_start: 0.6755 (tmm) cc_final: 0.6221 (tmm) REVERT: O 286 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6962 (mt-10) REVERT: V 1 MET cc_start: 0.4310 (ptm) cc_final: 0.2761 (tpt) REVERT: W 76 MET cc_start: 0.4294 (mmt) cc_final: 0.3826 (mmp) REVERT: c 62 GLU cc_start: 0.4023 (OUTLIER) cc_final: 0.3478 (pt0) outliers start: 58 outliers final: 25 residues processed: 496 average time/residue: 0.7753 time to fit residues: 670.7000 Evaluate side-chains 416 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 390 time to evaluate : 7.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 121 VAL Chi-restraints excluded: chain 1 residue 657 MET Chi-restraints excluded: chain 3 residue 366 HIS Chi-restraints excluded: chain 7 residue 85 ARG Chi-restraints excluded: chain 9 residue 41 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain U residue 351 PHE Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain c residue 62 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 490 optimal weight: 3.9990 chunk 273 optimal weight: 8.9990 chunk 734 optimal weight: 0.8980 chunk 601 optimal weight: 0.5980 chunk 243 optimal weight: 9.9990 chunk 884 optimal weight: 10.0000 chunk 955 optimal weight: 20.0000 chunk 787 optimal weight: 0.9990 chunk 876 optimal weight: 9.9990 chunk 301 optimal weight: 30.0000 chunk 709 optimal weight: 0.0060 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 ASN 8 67 GLN A 861 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN X 158 HIS c 32 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5491 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 87245 Z= 0.194 Angle : 0.562 9.787 119632 Z= 0.302 Chirality : 0.041 0.312 13413 Planarity : 0.004 0.045 13950 Dihedral : 19.725 178.009 14907 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.82 % Allowed : 8.28 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.09), residues: 9382 helix: 1.10 (0.08), residues: 4190 sheet: 0.05 (0.14), residues: 1188 loop : 0.05 (0.10), residues: 4004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 49 HIS 0.016 0.001 HIS A 313 PHE 0.029 0.001 PHE A 225 TYR 0.047 0.001 TYR 7 125 ARG 0.004 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 424 time to evaluate : 7.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 MET cc_start: -0.2236 (pmm) cc_final: -0.3342 (ptt) REVERT: 0 650 MET cc_start: -0.2840 (ptt) cc_final: -0.4093 (ttp) REVERT: 1 478 MET cc_start: 0.2102 (mmt) cc_final: 0.1353 (mmm) REVERT: 2 117 MET cc_start: -0.3139 (ptt) cc_final: -0.4254 (ptt) REVERT: 2 411 MET cc_start: -0.2692 (ttt) cc_final: -0.4399 (mtt) REVERT: 3 59 MET cc_start: -0.3438 (ttt) cc_final: -0.3682 (ttt) REVERT: 3 216 MET cc_start: -0.1240 (mtp) cc_final: -0.1565 (ptm) REVERT: 3 228 MET cc_start: -0.0348 (mmp) cc_final: -0.0868 (ttt) REVERT: 3 334 MET cc_start: 0.4113 (pmm) cc_final: 0.3410 (pmm) REVERT: 4 273 MET cc_start: -0.1648 (mmp) cc_final: -0.2038 (mmm) REVERT: A 329 MET cc_start: 0.6877 (mmp) cc_final: 0.5349 (ttm) REVERT: A 469 MET cc_start: 0.8247 (mtp) cc_final: 0.7718 (ttt) REVERT: A 687 ILE cc_start: 0.9122 (tp) cc_final: 0.8885 (tt) REVERT: A 1094 SER cc_start: 0.9478 (m) cc_final: 0.9161 (p) REVERT: B 121 SER cc_start: 0.9125 (m) cc_final: 0.8780 (p) REVERT: B 298 MET cc_start: 0.8162 (mmm) cc_final: 0.7876 (mpp) REVERT: B 733 MET cc_start: 0.8046 (mtt) cc_final: 0.7691 (mtt) REVERT: B 1046 THR cc_start: 0.8773 (m) cc_final: 0.8480 (p) REVERT: C 41 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7572 (mt-10) REVERT: E 135 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8534 (mm) REVERT: G 3 TYR cc_start: 0.5382 (m-80) cc_final: 0.4654 (m-80) REVERT: O 212 LEU cc_start: 0.6501 (tp) cc_final: 0.6270 (tp) REVERT: O 219 MET cc_start: 0.6515 (tmm) cc_final: 0.6060 (tmm) REVERT: O 286 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6929 (mt-10) REVERT: Q 121 ASN cc_start: 0.6453 (OUTLIER) cc_final: 0.5994 (t0) REVERT: V 1 MET cc_start: 0.4222 (ptm) cc_final: 0.2901 (tpt) REVERT: X 228 MET cc_start: 0.3051 (mtp) cc_final: 0.2645 (ttm) outliers start: 69 outliers final: 29 residues processed: 474 average time/residue: 0.7642 time to fit residues: 634.0149 Evaluate side-chains 410 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 379 time to evaluate : 8.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 315 VAL Chi-restraints excluded: chain 0 residue 417 THR Chi-restraints excluded: chain 1 residue 121 VAL Chi-restraints excluded: chain 1 residue 168 VAL Chi-restraints excluded: chain 1 residue 657 MET Chi-restraints excluded: chain 3 residue 366 HIS Chi-restraints excluded: chain 6 residue 43 VAL Chi-restraints excluded: chain 7 residue 81 ILE Chi-restraints excluded: chain 7 residue 85 ARG Chi-restraints excluded: chain 9 residue 41 LEU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain Q residue 121 ASN Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain U residue 351 PHE Chi-restraints excluded: chain V residue 8 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 873 optimal weight: 20.0000 chunk 664 optimal weight: 6.9990 chunk 458 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 422 optimal weight: 0.9980 chunk 593 optimal weight: 6.9990 chunk 887 optimal weight: 50.0000 chunk 939 optimal weight: 8.9990 chunk 463 optimal weight: 10.0000 chunk 841 optimal weight: 8.9990 chunk 253 optimal weight: 50.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 71 HIS 0 598 HIS ** 1 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 54 ASN 3 99 GLN 3 181 GLN ** 3 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 289 ASN ** 4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 905 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 461 GLN B 500 GLN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN B1101 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN M 140 ASN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5649 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 87245 Z= 0.572 Angle : 0.701 13.121 119632 Z= 0.366 Chirality : 0.045 0.237 13413 Planarity : 0.005 0.064 13950 Dihedral : 19.806 179.907 14907 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.37 % Allowed : 9.13 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.09), residues: 9382 helix: 0.96 (0.08), residues: 4172 sheet: -0.30 (0.14), residues: 1219 loop : -0.13 (0.10), residues: 3991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 0 421 HIS 0.011 0.002 HIS B 970 PHE 0.032 0.002 PHE B 918 TYR 0.037 0.002 TYR B 811 ARG 0.010 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 384 time to evaluate : 7.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 MET cc_start: -0.2523 (pmm) cc_final: -0.3634 (ptt) REVERT: 0 650 MET cc_start: -0.3185 (ptt) cc_final: -0.4408 (ttp) REVERT: 1 478 MET cc_start: 0.2180 (mmt) cc_final: 0.1685 (mmm) REVERT: 2 117 MET cc_start: -0.3289 (ptt) cc_final: -0.4389 (ptt) REVERT: 2 411 MET cc_start: -0.2980 (ttt) cc_final: -0.4639 (mtt) REVERT: 3 216 MET cc_start: -0.1345 (mtp) cc_final: -0.1661 (ptm) REVERT: 3 228 MET cc_start: 0.0117 (mmp) cc_final: -0.0833 (ttt) REVERT: 4 273 MET cc_start: -0.1845 (mmp) cc_final: -0.2053 (mmm) REVERT: 4 301 LEU cc_start: -0.3671 (OUTLIER) cc_final: -0.3904 (tt) REVERT: 7 265 MET cc_start: 0.4931 (mpp) cc_final: 0.4535 (mtm) REVERT: A 469 MET cc_start: 0.8539 (mtp) cc_final: 0.7713 (ttt) REVERT: A 1094 SER cc_start: 0.9493 (m) cc_final: 0.9133 (p) REVERT: B 121 SER cc_start: 0.9098 (m) cc_final: 0.8810 (p) REVERT: B 304 SER cc_start: 0.8741 (m) cc_final: 0.8157 (t) REVERT: B 508 MET cc_start: 0.9072 (mmt) cc_final: 0.8854 (mmm) REVERT: B 733 MET cc_start: 0.8715 (mtt) cc_final: 0.8435 (mtm) REVERT: B 1046 THR cc_start: 0.8843 (m) cc_final: 0.8217 (t) REVERT: C 41 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7582 (mt-10) REVERT: G 3 TYR cc_start: 0.5222 (m-80) cc_final: 0.5015 (m-80) REVERT: O 212 LEU cc_start: 0.6608 (tp) cc_final: 0.6401 (tp) REVERT: O 219 MET cc_start: 0.6563 (tmm) cc_final: 0.6139 (tmm) REVERT: V 1 MET cc_start: 0.4092 (ptm) cc_final: 0.2743 (tpt) outliers start: 115 outliers final: 64 residues processed: 473 average time/residue: 0.7723 time to fit residues: 642.4985 Evaluate side-chains 420 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 355 time to evaluate : 7.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 315 VAL Chi-restraints excluded: chain 0 residue 417 THR Chi-restraints excluded: chain 1 residue 121 VAL Chi-restraints excluded: chain 1 residue 309 VAL Chi-restraints excluded: chain 1 residue 657 MET Chi-restraints excluded: chain 1 residue 672 THR Chi-restraints excluded: chain 3 residue 348 ARG Chi-restraints excluded: chain 3 residue 366 HIS Chi-restraints excluded: chain 4 residue 301 LEU Chi-restraints excluded: chain 6 residue 43 VAL Chi-restraints excluded: chain 7 residue 9 CYS Chi-restraints excluded: chain 7 residue 81 ILE Chi-restraints excluded: chain 7 residue 85 ARG Chi-restraints excluded: chain 9 residue 41 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 128 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain U residue 351 PHE Chi-restraints excluded: chain V residue 8 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 782 optimal weight: 1.9990 chunk 533 optimal weight: 0.9980 chunk 13 optimal weight: 40.0000 chunk 699 optimal weight: 1.9990 chunk 387 optimal weight: 0.4980 chunk 801 optimal weight: 40.0000 chunk 649 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 479 optimal weight: 20.0000 chunk 843 optimal weight: 40.0000 chunk 237 optimal weight: 50.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN K 89 ASN O 167 ASN ** U 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5564 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 87245 Z= 0.233 Angle : 0.565 11.253 119632 Z= 0.299 Chirality : 0.040 0.250 13413 Planarity : 0.004 0.045 13950 Dihedral : 19.746 179.900 14907 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.12 % Allowed : 10.04 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 9382 helix: 1.13 (0.08), residues: 4173 sheet: -0.24 (0.14), residues: 1204 loop : -0.03 (0.10), residues: 4005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 49 HIS 0.008 0.001 HIS G 9 PHE 0.032 0.001 PHE 9 30 TYR 0.020 0.001 TYR 7 125 ARG 0.006 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 376 time to evaluate : 7.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 MET cc_start: -0.2599 (pmm) cc_final: -0.3600 (ptt) REVERT: 0 412 MET cc_start: -0.0443 (mtt) cc_final: -0.0881 (mtp) REVERT: 1 478 MET cc_start: 0.2068 (mmt) cc_final: 0.1568 (mmm) REVERT: 2 117 MET cc_start: -0.3289 (ptt) cc_final: -0.4407 (ptt) REVERT: 2 410 GLU cc_start: 0.0346 (OUTLIER) cc_final: -0.0296 (pt0) REVERT: 2 411 MET cc_start: -0.3025 (ttt) cc_final: -0.4695 (mtt) REVERT: 3 216 MET cc_start: -0.1594 (mtp) cc_final: -0.1928 (ptm) REVERT: 3 228 MET cc_start: 0.0087 (mmp) cc_final: -0.0596 (ttt) REVERT: 4 273 MET cc_start: -0.1689 (mmp) cc_final: -0.1970 (mmm) REVERT: 6 61 MET cc_start: 0.0772 (ttt) cc_final: 0.0428 (ttt) REVERT: 7 265 MET cc_start: 0.4971 (mpp) cc_final: 0.4571 (mtm) REVERT: 9 54 MET cc_start: 0.6415 (mtt) cc_final: 0.5944 (mtt) REVERT: A 329 MET cc_start: 0.6215 (mmp) cc_final: 0.5066 (ttp) REVERT: A 459 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7974 (t0) REVERT: A 469 MET cc_start: 0.8336 (mtp) cc_final: 0.7839 (ttt) REVERT: A 510 GLU cc_start: 0.7313 (mp0) cc_final: 0.6976 (mp0) REVERT: A 1094 SER cc_start: 0.9445 (m) cc_final: 0.9082 (p) REVERT: B 121 SER cc_start: 0.9040 (m) cc_final: 0.8794 (p) REVERT: B 298 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7618 (mmt) REVERT: B 304 SER cc_start: 0.8627 (m) cc_final: 0.8058 (t) REVERT: B 508 MET cc_start: 0.9060 (mmt) cc_final: 0.8797 (mmm) REVERT: B 733 MET cc_start: 0.8282 (mtt) cc_final: 0.7871 (mtt) REVERT: B 1046 THR cc_start: 0.8771 (m) cc_final: 0.8494 (p) REVERT: C 41 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7384 (mt-10) REVERT: J 1 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7635 (mpp) REVERT: O 219 MET cc_start: 0.6498 (tmm) cc_final: 0.6185 (tmm) REVERT: V 1 MET cc_start: 0.4068 (ptm) cc_final: 0.2747 (tpt) outliers start: 94 outliers final: 61 residues processed: 454 average time/residue: 0.7800 time to fit residues: 625.5595 Evaluate side-chains 420 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 355 time to evaluate : 7.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 191 ASP Chi-restraints excluded: chain 0 residue 315 VAL Chi-restraints excluded: chain 0 residue 417 THR Chi-restraints excluded: chain 1 residue 121 VAL Chi-restraints excluded: chain 1 residue 168 VAL Chi-restraints excluded: chain 1 residue 309 VAL Chi-restraints excluded: chain 1 residue 657 MET Chi-restraints excluded: chain 1 residue 672 THR Chi-restraints excluded: chain 2 residue 410 GLU Chi-restraints excluded: chain 2 residue 457 ILE Chi-restraints excluded: chain 2 residue 533 TYR Chi-restraints excluded: chain 3 residue 149 ASP Chi-restraints excluded: chain 3 residue 366 HIS Chi-restraints excluded: chain 6 residue 43 VAL Chi-restraints excluded: chain 7 residue 9 CYS Chi-restraints excluded: chain 7 residue 81 ILE Chi-restraints excluded: chain 7 residue 85 ARG Chi-restraints excluded: chain 9 residue 41 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 459 ASN Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain X residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 316 optimal weight: 50.0000 chunk 846 optimal weight: 3.9990 chunk 185 optimal weight: 50.0000 chunk 551 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 940 optimal weight: 3.9990 chunk 780 optimal weight: 0.5980 chunk 435 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 311 optimal weight: 30.0000 chunk 493 optimal weight: 0.0060 overall best weight: 2.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN K 89 ASN ** U 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5573 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 87245 Z= 0.259 Angle : 0.558 11.466 119632 Z= 0.295 Chirality : 0.040 0.237 13413 Planarity : 0.004 0.046 13950 Dihedral : 19.693 179.108 14907 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.20 % Allowed : 10.55 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.09), residues: 9382 helix: 1.26 (0.08), residues: 4181 sheet: -0.28 (0.14), residues: 1219 loop : -0.04 (0.10), residues: 3982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Q 164 HIS 0.008 0.001 HIS A 84 PHE 0.021 0.001 PHE 1 720 TYR 0.025 0.001 TYR G 3 ARG 0.006 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 366 time to evaluate : 7.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 MET cc_start: -0.2625 (pmm) cc_final: -0.3598 (ptt) REVERT: 0 412 MET cc_start: 0.0070 (mtt) cc_final: -0.0172 (mtt) REVERT: 1 478 MET cc_start: 0.2030 (mmt) cc_final: 0.1540 (mmm) REVERT: 1 545 MET cc_start: 0.6601 (mmt) cc_final: 0.6339 (mmm) REVERT: 2 117 MET cc_start: -0.3452 (ptt) cc_final: -0.4525 (ptt) REVERT: 2 411 MET cc_start: -0.3074 (ttt) cc_final: -0.4765 (mtt) REVERT: 3 216 MET cc_start: -0.1692 (mtp) cc_final: -0.1966 (ptm) REVERT: 3 228 MET cc_start: 0.0241 (mmp) cc_final: -0.0500 (ttt) REVERT: 4 273 MET cc_start: -0.1696 (mmp) cc_final: -0.1959 (mmm) REVERT: 7 265 MET cc_start: 0.4657 (mpp) cc_final: 0.4284 (mtm) REVERT: 8 118 MET cc_start: -0.2272 (ppp) cc_final: -0.2660 (ppp) REVERT: 9 54 MET cc_start: 0.6608 (mtt) cc_final: 0.6127 (mtt) REVERT: A 329 MET cc_start: 0.6639 (mmp) cc_final: 0.5089 (ttp) REVERT: A 469 MET cc_start: 0.8349 (mtp) cc_final: 0.7940 (ttt) REVERT: A 510 GLU cc_start: 0.7286 (mp0) cc_final: 0.7085 (mp0) REVERT: A 687 ILE cc_start: 0.9090 (tp) cc_final: 0.8854 (tt) REVERT: A 1094 SER cc_start: 0.9450 (m) cc_final: 0.9101 (p) REVERT: A 1279 MET cc_start: 0.0183 (mmt) cc_final: -0.0422 (mmt) REVERT: B 121 SER cc_start: 0.9075 (m) cc_final: 0.8836 (p) REVERT: B 298 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7611 (mmt) REVERT: B 304 SER cc_start: 0.8646 (m) cc_final: 0.8084 (t) REVERT: B 508 MET cc_start: 0.9065 (mmt) cc_final: 0.8818 (mmm) REVERT: B 733 MET cc_start: 0.8373 (mtt) cc_final: 0.8035 (mtm) REVERT: B 1046 THR cc_start: 0.8732 (m) cc_final: 0.8191 (t) REVERT: C 41 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7390 (mt-10) REVERT: J 1 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7715 (mpp) REVERT: O 219 MET cc_start: 0.6381 (tmm) cc_final: 0.6126 (tmm) REVERT: V 1 MET cc_start: 0.4135 (ptm) cc_final: 0.2773 (tpt) outliers start: 100 outliers final: 74 residues processed: 448 average time/residue: 0.7770 time to fit residues: 615.7015 Evaluate side-chains 431 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 355 time to evaluate : 7.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 191 ASP Chi-restraints excluded: chain 0 residue 315 VAL Chi-restraints excluded: chain 0 residue 417 THR Chi-restraints excluded: chain 0 residue 602 ILE Chi-restraints excluded: chain 1 residue 121 VAL Chi-restraints excluded: chain 1 residue 309 VAL Chi-restraints excluded: chain 1 residue 657 MET Chi-restraints excluded: chain 2 residue 457 ILE Chi-restraints excluded: chain 2 residue 533 TYR Chi-restraints excluded: chain 3 residue 149 ASP Chi-restraints excluded: chain 3 residue 366 HIS Chi-restraints excluded: chain 3 residue 450 ASP Chi-restraints excluded: chain 5 residue 11 LEU Chi-restraints excluded: chain 7 residue 9 CYS Chi-restraints excluded: chain 7 residue 85 ARG Chi-restraints excluded: chain 8 residue 240 MET Chi-restraints excluded: chain 9 residue 41 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 128 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain U residue 351 PHE Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain X residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 906 optimal weight: 20.0000 chunk 106 optimal weight: 50.0000 chunk 535 optimal weight: 0.9980 chunk 686 optimal weight: 8.9990 chunk 532 optimal weight: 0.8980 chunk 791 optimal weight: 50.0000 chunk 525 optimal weight: 0.9990 chunk 936 optimal weight: 6.9990 chunk 586 optimal weight: 1.9990 chunk 571 optimal weight: 0.9980 chunk 432 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 ASN 7 129 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN R 14 GLN ** U 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5536 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 87245 Z= 0.176 Angle : 0.535 11.209 119632 Z= 0.282 Chirality : 0.039 0.241 13413 Planarity : 0.003 0.044 13950 Dihedral : 19.611 178.338 14907 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.14 % Allowed : 11.01 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.09), residues: 9382 helix: 1.36 (0.08), residues: 4191 sheet: -0.19 (0.15), residues: 1203 loop : -0.04 (0.10), residues: 3988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 49 HIS 0.006 0.001 HIS 1 37 PHE 0.024 0.001 PHE 1 720 TYR 0.020 0.001 TYR 3 151 ARG 0.009 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 374 time to evaluate : 7.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 MET cc_start: -0.2320 (pmm) cc_final: -0.3368 (ptt) REVERT: 0 412 MET cc_start: 0.0121 (mtt) cc_final: -0.0138 (mtt) REVERT: 1 478 MET cc_start: 0.1957 (mmt) cc_final: 0.1471 (mmm) REVERT: 2 117 MET cc_start: -0.3373 (ptt) cc_final: -0.4480 (ptt) REVERT: 2 410 GLU cc_start: 0.0514 (OUTLIER) cc_final: -0.0314 (pt0) REVERT: 2 411 MET cc_start: -0.3212 (ttt) cc_final: -0.4878 (mtt) REVERT: 3 57 MET cc_start: -0.0276 (ttt) cc_final: -0.0676 (ttt) REVERT: 3 216 MET cc_start: -0.1689 (mtp) cc_final: -0.2129 (ptm) REVERT: 3 228 MET cc_start: 0.0014 (mmp) cc_final: -0.0648 (ttt) REVERT: 4 273 MET cc_start: -0.1753 (mmp) cc_final: -0.2009 (mmm) REVERT: 7 265 MET cc_start: 0.4710 (mpp) cc_final: 0.4359 (mtm) REVERT: 9 32 CYS cc_start: 0.1693 (OUTLIER) cc_final: 0.1451 (t) REVERT: 9 54 MET cc_start: 0.6618 (mtt) cc_final: 0.6117 (mtt) REVERT: A 248 MET cc_start: 0.6443 (tpt) cc_final: 0.6152 (tpt) REVERT: A 329 MET cc_start: 0.6664 (mmp) cc_final: 0.5163 (ttp) REVERT: A 469 MET cc_start: 0.8229 (mtp) cc_final: 0.8021 (ttt) REVERT: A 510 GLU cc_start: 0.7274 (mp0) cc_final: 0.7035 (mp0) REVERT: A 687 ILE cc_start: 0.9067 (tp) cc_final: 0.8835 (tt) REVERT: A 1094 SER cc_start: 0.9431 (m) cc_final: 0.9096 (p) REVERT: A 1279 MET cc_start: 0.0055 (mmt) cc_final: -0.0430 (mmt) REVERT: B 121 SER cc_start: 0.9059 (m) cc_final: 0.8778 (p) REVERT: B 298 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7864 (mpp) REVERT: B 304 SER cc_start: 0.8610 (m) cc_final: 0.7996 (t) REVERT: B 365 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8815 (tt) REVERT: B 508 MET cc_start: 0.9058 (mmt) cc_final: 0.8795 (mmm) REVERT: B 733 MET cc_start: 0.8150 (mtt) cc_final: 0.7785 (mtt) REVERT: B 976 MET cc_start: 0.7816 (mtm) cc_final: 0.7363 (mtm) REVERT: B 1046 THR cc_start: 0.8768 (m) cc_final: 0.8501 (p) REVERT: C 41 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7468 (mt-10) REVERT: J 1 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7699 (mpp) REVERT: V 1 MET cc_start: 0.4257 (ptm) cc_final: 0.2824 (tpt) outliers start: 95 outliers final: 68 residues processed: 450 average time/residue: 0.7591 time to fit residues: 604.6761 Evaluate side-chains 435 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 362 time to evaluate : 7.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 191 ASP Chi-restraints excluded: chain 0 residue 315 VAL Chi-restraints excluded: chain 0 residue 417 THR Chi-restraints excluded: chain 0 residue 602 ILE Chi-restraints excluded: chain 1 residue 121 VAL Chi-restraints excluded: chain 1 residue 168 VAL Chi-restraints excluded: chain 1 residue 309 VAL Chi-restraints excluded: chain 1 residue 657 MET Chi-restraints excluded: chain 2 residue 410 GLU Chi-restraints excluded: chain 2 residue 457 ILE Chi-restraints excluded: chain 2 residue 533 TYR Chi-restraints excluded: chain 3 residue 149 ASP Chi-restraints excluded: chain 3 residue 366 HIS Chi-restraints excluded: chain 5 residue 11 LEU Chi-restraints excluded: chain 6 residue 43 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 7 residue 9 CYS Chi-restraints excluded: chain 7 residue 85 ARG Chi-restraints excluded: chain 8 residue 240 MET Chi-restraints excluded: chain 9 residue 32 CYS Chi-restraints excluded: chain 9 residue 41 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain U residue 351 PHE Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain g residue 26 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 579 optimal weight: 0.7980 chunk 374 optimal weight: 8.9990 chunk 559 optimal weight: 0.9990 chunk 282 optimal weight: 50.0000 chunk 184 optimal weight: 50.0000 chunk 181 optimal weight: 9.9990 chunk 595 optimal weight: 7.9990 chunk 638 optimal weight: 10.0000 chunk 463 optimal weight: 30.0000 chunk 87 optimal weight: 7.9990 chunk 736 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A 861 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 95 GLN K 89 ASN ** U 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5632 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 87245 Z= 0.439 Angle : 0.622 12.747 119632 Z= 0.324 Chirality : 0.042 0.235 13413 Planarity : 0.004 0.049 13950 Dihedral : 19.628 177.493 14907 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.23 % Allowed : 11.39 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.09), residues: 9382 helix: 1.26 (0.08), residues: 4196 sheet: -0.29 (0.15), residues: 1212 loop : -0.08 (0.10), residues: 3974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 453 HIS 0.008 0.001 HIS A 84 PHE 0.032 0.002 PHE 1 720 TYR 0.025 0.001 TYR H 142 ARG 0.010 0.000 ARG 7 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 357 time to evaluate : 7.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 MET cc_start: -0.2916 (pmm) cc_final: -0.4018 (ptt) REVERT: 1 478 MET cc_start: 0.1999 (mmt) cc_final: 0.1573 (mmm) REVERT: 2 117 MET cc_start: -0.3244 (ptt) cc_final: -0.4363 (ptt) REVERT: 2 410 GLU cc_start: 0.0620 (OUTLIER) cc_final: -0.0034 (pt0) REVERT: 2 411 MET cc_start: -0.3277 (ttt) cc_final: -0.4264 (mtp) REVERT: 3 216 MET cc_start: -0.1670 (mtp) cc_final: -0.2153 (ptm) REVERT: 3 228 MET cc_start: 0.0165 (mmp) cc_final: -0.0517 (ttt) REVERT: 4 57 MET cc_start: 0.0292 (pmm) cc_final: 0.0079 (pmm) REVERT: 4 273 MET cc_start: -0.1740 (mmp) cc_final: -0.2219 (mmm) REVERT: 5 178 MET cc_start: 0.3165 (tpp) cc_final: 0.2739 (tmm) REVERT: 7 265 MET cc_start: 0.4694 (mpp) cc_final: 0.4341 (mtm) REVERT: 9 54 MET cc_start: 0.6601 (mtt) cc_final: 0.6049 (mtt) REVERT: A 329 MET cc_start: 0.6870 (mmp) cc_final: 0.5166 (ttm) REVERT: A 469 MET cc_start: 0.8459 (mtp) cc_final: 0.7926 (ttt) REVERT: A 899 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: A 1094 SER cc_start: 0.9477 (m) cc_final: 0.9134 (p) REVERT: A 1279 MET cc_start: 0.0178 (mmt) cc_final: -0.0085 (mmt) REVERT: B 121 SER cc_start: 0.9068 (m) cc_final: 0.8810 (p) REVERT: B 298 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7599 (mmt) REVERT: B 304 SER cc_start: 0.8740 (m) cc_final: 0.8180 (t) REVERT: B 365 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8979 (tt) REVERT: B 508 MET cc_start: 0.9149 (mmt) cc_final: 0.8888 (mmm) REVERT: B 733 MET cc_start: 0.8551 (mtt) cc_final: 0.8157 (mtm) REVERT: B 1046 THR cc_start: 0.8738 (m) cc_final: 0.8196 (t) REVERT: C 41 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7459 (mt-10) REVERT: J 1 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7702 (mpp) REVERT: V 1 MET cc_start: 0.4453 (ptm) cc_final: 0.2937 (tpt) REVERT: W 110 MET cc_start: 0.6010 (mmt) cc_final: 0.5755 (mmt) outliers start: 103 outliers final: 82 residues processed: 444 average time/residue: 0.7784 time to fit residues: 617.8429 Evaluate side-chains 435 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 348 time to evaluate : 7.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 191 ASP Chi-restraints excluded: chain 0 residue 315 VAL Chi-restraints excluded: chain 0 residue 417 THR Chi-restraints excluded: chain 0 residue 602 ILE Chi-restraints excluded: chain 1 residue 121 VAL Chi-restraints excluded: chain 1 residue 168 VAL Chi-restraints excluded: chain 1 residue 309 VAL Chi-restraints excluded: chain 1 residue 657 MET Chi-restraints excluded: chain 2 residue 410 GLU Chi-restraints excluded: chain 2 residue 457 ILE Chi-restraints excluded: chain 2 residue 533 TYR Chi-restraints excluded: chain 3 residue 149 ASP Chi-restraints excluded: chain 3 residue 366 HIS Chi-restraints excluded: chain 3 residue 450 ASP Chi-restraints excluded: chain 6 residue 43 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 7 residue 9 CYS Chi-restraints excluded: chain 7 residue 85 ARG Chi-restraints excluded: chain 8 residue 240 MET Chi-restraints excluded: chain 9 residue 41 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1112 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 128 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain U residue 351 PHE Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain g residue 26 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 852 optimal weight: 30.0000 chunk 897 optimal weight: 10.0000 chunk 818 optimal weight: 5.9990 chunk 873 optimal weight: 30.0000 chunk 525 optimal weight: 2.9990 chunk 380 optimal weight: 0.7980 chunk 685 optimal weight: 0.8980 chunk 267 optimal weight: 1.9990 chunk 788 optimal weight: 30.0000 chunk 825 optimal weight: 90.0000 chunk 869 optimal weight: 40.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 260 ASN ** 4 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 126 GLN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS ** U 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 87245 Z= 0.254 Angle : 0.559 13.079 119632 Z= 0.293 Chirality : 0.040 0.241 13413 Planarity : 0.004 0.044 13950 Dihedral : 19.597 177.082 14907 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.08 % Allowed : 11.68 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.09), residues: 9382 helix: 1.33 (0.08), residues: 4204 sheet: -0.28 (0.14), residues: 1229 loop : -0.06 (0.10), residues: 3949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 49 HIS 0.007 0.001 HIS A 84 PHE 0.052 0.001 PHE 1 720 TYR 0.020 0.001 TYR 3 151 ARG 0.004 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 354 time to evaluate : 7.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 MET cc_start: -0.2974 (pmm) cc_final: -0.3985 (ptt) REVERT: 0 412 MET cc_start: -0.0240 (mtt) cc_final: -0.0650 (mtt) REVERT: 1 478 MET cc_start: 0.2082 (mmt) cc_final: 0.1637 (mmm) REVERT: 2 117 MET cc_start: -0.3382 (ptt) cc_final: -0.4504 (ptt) REVERT: 2 410 GLU cc_start: 0.0474 (OUTLIER) cc_final: 0.0039 (pt0) REVERT: 2 411 MET cc_start: -0.3266 (ttt) cc_final: -0.4212 (mtp) REVERT: 3 216 MET cc_start: -0.1604 (mtp) cc_final: -0.2238 (ptm) REVERT: 3 228 MET cc_start: 0.0124 (mmp) cc_final: -0.0615 (ttt) REVERT: 4 273 MET cc_start: -0.1809 (mmp) cc_final: -0.2277 (mmm) REVERT: 7 265 MET cc_start: 0.4823 (mpp) cc_final: 0.4493 (mtm) REVERT: 8 94 MET cc_start: -0.1036 (ttt) cc_final: -0.1418 (ttt) REVERT: 9 54 MET cc_start: 0.6723 (mtt) cc_final: 0.6173 (mtt) REVERT: A 329 MET cc_start: 0.6741 (mmp) cc_final: 0.5140 (ttm) REVERT: A 510 GLU cc_start: 0.7260 (mp0) cc_final: 0.7009 (mp0) REVERT: A 899 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: A 1094 SER cc_start: 0.9431 (m) cc_final: 0.9082 (p) REVERT: A 1412 MET cc_start: 0.7538 (mmm) cc_final: 0.7099 (mmm) REVERT: B 121 SER cc_start: 0.9078 (m) cc_final: 0.8807 (p) REVERT: B 297 MET cc_start: 0.6854 (mmt) cc_final: 0.6546 (mmt) REVERT: B 298 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7798 (mpp) REVERT: B 300 MET cc_start: 0.6477 (mmm) cc_final: 0.6020 (mmm) REVERT: B 304 SER cc_start: 0.8687 (m) cc_final: 0.8128 (t) REVERT: B 365 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8825 (tt) REVERT: B 508 MET cc_start: 0.9097 (mmt) cc_final: 0.8829 (mmm) REVERT: B 733 MET cc_start: 0.8311 (mtt) cc_final: 0.8040 (mtt) REVERT: B 976 MET cc_start: 0.7833 (mtm) cc_final: 0.7590 (mtm) REVERT: B 1046 THR cc_start: 0.8774 (m) cc_final: 0.8275 (t) REVERT: C 41 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7365 (mt-10) REVERT: J 1 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7671 (mpp) REVERT: V 1 MET cc_start: 0.4361 (ptm) cc_final: 0.2871 (tpt) outliers start: 90 outliers final: 74 residues processed: 432 average time/residue: 0.7601 time to fit residues: 584.0479 Evaluate side-chains 427 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 348 time to evaluate : 7.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 191 ASP Chi-restraints excluded: chain 0 residue 417 THR Chi-restraints excluded: chain 0 residue 602 ILE Chi-restraints excluded: chain 1 residue 121 VAL Chi-restraints excluded: chain 1 residue 168 VAL Chi-restraints excluded: chain 1 residue 309 VAL Chi-restraints excluded: chain 1 residue 657 MET Chi-restraints excluded: chain 2 residue 410 GLU Chi-restraints excluded: chain 2 residue 457 ILE Chi-restraints excluded: chain 2 residue 533 TYR Chi-restraints excluded: chain 3 residue 149 ASP Chi-restraints excluded: chain 3 residue 366 HIS Chi-restraints excluded: chain 3 residue 450 ASP Chi-restraints excluded: chain 6 residue 43 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 7 residue 9 CYS Chi-restraints excluded: chain 7 residue 85 ARG Chi-restraints excluded: chain 8 residue 240 MET Chi-restraints excluded: chain 9 residue 41 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1112 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain U residue 351 PHE Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain g residue 26 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 573 optimal weight: 0.6980 chunk 923 optimal weight: 30.0000 chunk 563 optimal weight: 0.7980 chunk 437 optimal weight: 0.8980 chunk 641 optimal weight: 3.9990 chunk 968 optimal weight: 10.0000 chunk 891 optimal weight: 50.0000 chunk 771 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 595 optimal weight: 5.9990 chunk 472 optimal weight: 5.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 260 ASN ** 4 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 HIS ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 ASN ** U 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 87245 Z= 0.255 Angle : 0.562 13.762 119632 Z= 0.293 Chirality : 0.040 0.237 13413 Planarity : 0.004 0.045 13950 Dihedral : 19.566 176.913 14907 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.11 % Allowed : 11.68 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.09), residues: 9382 helix: 1.37 (0.08), residues: 4201 sheet: -0.28 (0.14), residues: 1219 loop : -0.03 (0.10), residues: 3962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 49 HIS 0.028 0.001 HIS B 842 PHE 0.047 0.001 PHE 1 720 TYR 0.021 0.001 TYR 1 674 ARG 0.009 0.000 ARG O 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18764 Ramachandran restraints generated. 9382 Oldfield, 0 Emsley, 9382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 351 time to evaluate : 7.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 MET cc_start: -0.3026 (pmm) cc_final: -0.3838 (ptt) REVERT: 0 412 MET cc_start: -0.0378 (mtt) cc_final: -0.0815 (mtt) REVERT: 1 478 MET cc_start: 0.2083 (mmt) cc_final: 0.1630 (mmm) REVERT: 2 117 MET cc_start: -0.3664 (ptt) cc_final: -0.4858 (ptt) REVERT: 2 411 MET cc_start: -0.3320 (ttt) cc_final: -0.4100 (mtp) REVERT: 3 216 MET cc_start: -0.1556 (mtp) cc_final: -0.2086 (ptm) REVERT: 3 228 MET cc_start: 0.0142 (mmp) cc_final: -0.0582 (ttt) REVERT: 7 265 MET cc_start: 0.4824 (mpp) cc_final: 0.4513 (mtm) REVERT: 8 94 MET cc_start: -0.0977 (ttt) cc_final: -0.1298 (ttt) REVERT: 9 54 MET cc_start: 0.6749 (mtt) cc_final: 0.6182 (mtt) REVERT: A 329 MET cc_start: 0.6751 (mmp) cc_final: 0.5123 (ttm) REVERT: A 510 GLU cc_start: 0.7227 (mp0) cc_final: 0.6990 (mp0) REVERT: A 687 ILE cc_start: 0.9073 (tp) cc_final: 0.8841 (tt) REVERT: A 899 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: A 1094 SER cc_start: 0.9451 (m) cc_final: 0.9112 (p) REVERT: A 1412 MET cc_start: 0.7524 (mmm) cc_final: 0.7036 (mmm) REVERT: B 121 SER cc_start: 0.9057 (m) cc_final: 0.8817 (p) REVERT: B 298 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7747 (mpp) REVERT: B 304 SER cc_start: 0.8699 (m) cc_final: 0.8146 (t) REVERT: B 365 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8833 (tt) REVERT: B 508 MET cc_start: 0.9113 (mmt) cc_final: 0.8842 (mmm) REVERT: B 733 MET cc_start: 0.8371 (mtt) cc_final: 0.7988 (mtt) REVERT: B 976 MET cc_start: 0.7708 (mtm) cc_final: 0.7302 (mtm) REVERT: B 1046 THR cc_start: 0.8700 (m) cc_final: 0.8174 (t) REVERT: C 41 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7390 (mt-10) REVERT: J 1 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7665 (mpp) REVERT: V 1 MET cc_start: 0.4332 (ptm) cc_final: 0.2849 (tpt) REVERT: W 110 MET cc_start: 0.5832 (mmt) cc_final: 0.5622 (mmt) outliers start: 93 outliers final: 79 residues processed: 430 average time/residue: 0.8022 time to fit residues: 614.4231 Evaluate side-chains 430 residues out of total 8384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 347 time to evaluate : 7.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 191 ASP Chi-restraints excluded: chain 0 residue 315 VAL Chi-restraints excluded: chain 0 residue 417 THR Chi-restraints excluded: chain 0 residue 602 ILE Chi-restraints excluded: chain 1 residue 121 VAL Chi-restraints excluded: chain 1 residue 168 VAL Chi-restraints excluded: chain 1 residue 309 VAL Chi-restraints excluded: chain 1 residue 657 MET Chi-restraints excluded: chain 1 residue 673 ASP Chi-restraints excluded: chain 2 residue 533 TYR Chi-restraints excluded: chain 3 residue 149 ASP Chi-restraints excluded: chain 3 residue 366 HIS Chi-restraints excluded: chain 3 residue 450 ASP Chi-restraints excluded: chain 6 residue 43 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 7 residue 9 CYS Chi-restraints excluded: chain 7 residue 85 ARG Chi-restraints excluded: chain 8 residue 240 MET Chi-restraints excluded: chain 9 residue 41 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 128 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain U residue 351 PHE Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain g residue 26 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 612 optimal weight: 0.9980 chunk 821 optimal weight: 7.9990 chunk 236 optimal weight: 50.0000 chunk 711 optimal weight: 0.5980 chunk 113 optimal weight: 20.0000 chunk 214 optimal weight: 20.0000 chunk 772 optimal weight: 0.3980 chunk 323 optimal weight: 30.0000 chunk 793 optimal weight: 0.0980 chunk 97 optimal weight: 40.0000 chunk 142 optimal weight: 9.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 HIS ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN O 327 ASN ** U 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.141921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.129084 restraints weight = 327085.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.126436 restraints weight = 376945.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.124228 restraints weight = 399955.147| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5578 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 87245 Z= 0.218 Angle : 0.553 20.084 119632 Z= 0.287 Chirality : 0.040 0.241 13413 Planarity : 0.004 0.053 13950 Dihedral : 19.528 176.726 14907 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.05 % Allowed : 11.92 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.09), residues: 9382 helix: 1.41 (0.08), residues: 4204 sheet: -0.23 (0.15), residues: 1202 loop : -0.02 (0.10), residues: 3976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 49 HIS 0.020 0.001 HIS B 842 PHE 0.045 0.001 PHE 1 720 TYR 0.023 0.001 TYR 0 534 ARG 0.013 0.000 ARG C 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12886.20 seconds wall clock time: 233 minutes 8.25 seconds (13988.25 seconds total)